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Artemis Software List

Summary table of software installed on Artemis

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Machine Learning and Data Mining

3D-Caffe, Caffe, Caffe2, libgpuarray, MXNet, OpenCV, Root, Stxxl, TensorFlow, Torch

CFD and Engineering

Abaqus, ANSYS, AnsysEM, CGNS, Gmsh, Gurobi, LS-DYNA, LS-PrePost, Nastran, ODE, OpenFOAM, Yade

Bioinformatics

Abricate, Abyss, Abyss-mpi, AdapterRemoval, AfterQC, Aligngraph, AlleleSeq, Allpathslg, AmrPlusPlus, AnnotSV, AnnotSV, Annovar, Aragorn, armatus, Artemis, ArtificialFastqGenerator, Augustus, bam-readcount, Bambamc, Bamtools, bamUtil, barrnap, BASE, Basespace, BatMeth, BayesAss, Bbmap, BCFtools, Bcl2fastq, Beagle, Beast, BEDOPS, Bedtools, biobambam2, Biopieces, Bismark, Blasr, Blast, BLAST+, Blat, BlobTools, Bowtie, Bowtie2, bpp, Bracken, BRAKER1, BRAKER2, Brig, Busco, Bvatools, BWA, CAFExp, Canu, Cap3, CCMetagen, Cd-Hit, Cell Ranger, Centrifuge, Chimera, Chimeraslayer, ChunkChromosome, ClinSV, Clonalframeml, Clustal Omega, Clustal W/X, CNVnator, Codonphyml, coevol, Cortex, Crest, Cufflinks, Cutadapt, Delly, DETONATE, Diamond, Drive5, dx-toolkit, Ea-Utils, EDirect, EffectorP, Emboss, EMMAX, EPA-ng, Epacts, EVidenceModeler, ExaBayes, EXCAVATOR2tool, exonerate, Falcon, Falcon-Unzip, FastME, Fastml, fastp, fastPHASE, FastQC, fastQValidator, Fasttree, Fastx, fgbio, FImpute, Flash, fqgrep, fqtools, FragGeneScan, FRANz, freebayes, funannotate, FUSTr, gatb, Gatk, Gblocks, gcta, gem-tools, Gemma, GeneMark-ES, Genomemasker, GenomeTools, Gess, giremi, gmap, GPS-Lipid, GraPhlAn, GraPhlAn, GRIDSS, GTFTools, Gubbins, Haddock, hapcut, Hapcut, Hapflow, haplotyper, Haploview, Hapsembler, Hh-Suite, HiC-bench, HiCUP, HISAT2, hlascan, hmftools, Hmmer, Homer, hotspotter, HTSlib, I-Tasser, Idba, idp, Igvtools, IMPUTE2, Infernal, InterProScan, IQ-TREE, Is_Mapper, ITSx, Iva, Jaspa, Jellyfish, Juicer, Kalign, kallisto, Kat, kentutils, KMA, Kmc, KohGPI, Kraken, Kraken2, KronaTools, kSNP, LAST, LASTZ, libmaus2, lighter, Lofreq, longranger, lordec, lumpy-sv, MACH, MaCH-Admix, MAFFT, Magic-BLAST, Maker, Manta, MARVEL, Mash, MATAM, Mauve, MaxBin2, Medusa, Megacc, Megahit, megan, MELT, Meme, MetaBAT, MetaPhlAn2, MetaSim, Metatissue, MetaVelvet, meth_progs, Methpipe, MethylDackel, Migrate-N, minced, Minimac2, Minimac4, Minimap2, Mira, Mirdeep2, MISTReSS, Mlst, Mothur, mpiBWA, Mrbayes, Mugsy, Mummer3, Mummer4, Mutect, Mykrobe-Predictor, NanoOk, Nanopolish, NCBI C++ Toolkit, Newick-Utils, Norgal, Nullarbor, oases, OmegaPlus, OrthoFiller, OrthoFinder, Paml, pandaseq, Pblat, Pear, PennCNV, pgdspider, phase, Pheniqs, Phobius, PHYLIP, PhyloBayes, Phyml, Picard, Pilon, Pindel, Pipits, Platypus, PLINK, PneumoCaT, PneumoCaT, pplacer, Prank, Preseq, Prinseq, Prodigal, Prokka, ProteinOrtho, PSIPRED, PSMC, Purge Haplotigs, Qiime, Qorts, Qualimap, QUAST, QuickTree, Racon, Ragout, RAiSD, Ray, Rdpclassifier, Readseq, REAPR, Reddog, Repeatmasker, Repeatmodeler, RepeatScout, Rmats, Rnammer, Roary, Rosetta, RSEM, Salmon, sam2bam, Sambamba, Samblaster, samclip, Samtools, scotti, SecretomeP, selscan, SeqKit, seqOutBias, Seqtk, sff2fastq, Sga, SHAPEIT, Shorah, ShortStack, shovill, Sibelia, Signalp, SiLiX, SKESA, SLiMSuite, Smalt, SMRT, SMRTtools, SNAP, Snippy, snp-dists, SNP-sites, SnpEff, SNPhylo, SOAPdenovo2, SortMeRNA, Spades, SpeedSeq, Sratoolkit, STACKS, Stampy, Star, Strainseeker, Strelka, Stringtie, subread, Subread, Supernova, Surpi, Svtyper, sweed, SweepFinder2, SynerClust, Tabix, tantan, taxator-tk, Tbl2Asn, Tophat, Tracer, Transdecoder, Trim Galore, trimAl, Trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Genome Browser, Usearch, UVP, Varscan, VaST, vcf2diploid, Vcftools, Velvet, VelvetOptimiser, ViennaRNA, Vmatch, Vsearch, WALT, Wgs, wgsim, XHMM, XP-EHH

Medicine

afni, Amos, ANTs, ASHS, c3d, camino, Conn, dcm2niix, Dcmtk, DTI-TK, Fix, Freesurfer, Fsl, Gamos, Gate, MIPAV, MRtrix3, rtk

Command line utility

Ag, Aria2, Autoconf, Automake, bzip2, curl, Cyberduck, gawk, GDC-Client, gengetopt, Gettext, gtextutils, jq, Libunistring, Lzma, M4, Mawk, Pandoc, pigz, RapidJSON, Readline, Snappy, Xdrfile, Zstd

Code Development Utilities

Anaconda, Anaconda2, Argtable2, Bazel, Binutils, Bison, Cmake, Dbus, Dbus-Glib, Doxygen, emacs, Expat, Flex, Fontconfig, Gdl, Gflags, Git, Glib, Graphviz, Guile, Icmake, Icu, Jupyter, Leveldb, Libcroco, Libcurl, Libffi, Libgc, Libmng, Libspatialite, Libspectre, Libtau, Libtiff, Libtool, Libxml2, Libxslt, Luabind, Luajit, Maven, Mercurial, Ncurses, Node, Pango, Pcre, Pcre2, Protobuf, Raxml, Raxmls, Scons, Slang, Sparsehash, Spatialite, Sphinx, Subversion, Swig, tre, Udunits, Vcflib, Xmlto, Yasm

Other

Ann, Epimine, Gephi, Glog, Harfbuzz, libevent, Lmdb, Modeller, Mono, MTBseq, OpenSSL, Osrm, pugixml, Readosm, SDL, SDL_image, Singularity, tmux, yaml-cpp

Physics

Ant, GadgetViewer, Geant4, Tomographer, wcslib

Math libraries

Armadillo, Arpack-Ng, Atlas, Baps, Blas, Boost, Cblas, Cddlib, CGAL, Clhep, Eigen, Eigenvalue SoLvers for Petaflop-Applications (ELPA), FFTW, Geos, GHMM, GMP, Gsl, GTS, Highwayhash, HYPRE, Lapack, Libmatheval, Libsodium, libspatialindex, Loki, Lsd, METIS, MPC, MPFR, Nettle, Nlopt, OpenBLAS, Qhull, Routino, ScaLAPACK, Scotch, SLEPc, Suitesparse

Simulation and Modelling

Biogeme, Jags, Mcl, Netgen, Netlogo, Underworld 2

Graphics

Cairo, cairomm, Circos, Ffmpeg, FLTK, FreeGLUT, Freetype, Ghostscript, Gnuplot, Graphicsmagick, Idl, IL, Imagej, Imagemagick, Imp, Jasper, libfreeimage, Libgd, Libjpeg, Libpng, libQGLViewer, MathGL, MayaVi, OpenJPEG, OpenSlide, Paraview, Photoscan-Pro, Pixman, Plplot, Poppler, Povray, Pslib, Simple, Visit, Vmd, Vtk

File formats and data management packages

CFITSIO, Freexl, GL2PS, HDF5, Hiredis, Intltool, Libelf, Ncview, NetCDF, Xz, Zlib

Parallel Programming Libraries/Tools

Cuda, Cuda2, Gperftools, HPC GridRunner, Intel-MPI, Mpich, MVAPICH2, OpenMPI-gcc, OpenMPI-Intel, OpenMPI-PGI, Parallel, Spark, Tbb, Zeromq

Chemistry

Dlpoly, Exciting, gaussian, Gromacs, Gromacs-Plumed, Hoomd, Lammps, LIGGGHTS-PUBLIC, LIGGGHTS-with-bonds, Macs, Molpro, NAMD, ORCA, Plumed, Pymol, Qe, Siesta, XCrySDen

Network Access & Grid Services

Ec2-Api-Tools, Libfabric

Math Libraries

Armadillo, Arpack-Ng, Atlas, Baps, Blas, Boost, Cblas, Cddlib, CGAL, Clhep, Eigen, Eigenvalue SoLvers for Petaflop-Applications (ELPA), FFTW, Geos, GHMM, GMP, Gsl, GTS, Highwayhash, HYPRE, Lapack, Libmatheval, Libsodium, libspatialindex, Loki, Lsd, METIS, MPC, MPFR, Nettle, Nlopt, OpenBLAS, Qhull, Routino, ScaLAPACK, Scotch, SLEPc, Suitesparse

Mathematics and Statistics

FEniCS, HEALPix, Macaulay2, Mathematica, Matlab, MCR, petsc, PHCpack, SAS, SUNDIALS

Compilers

gcc, Go, Intel, Java, NASM, Pgi

Geospatial Tools

Gdal, Proj, Proj.4, Rgdal, VAPOR, Virtualpg

Debuggers, Profilers and Simulators

Gdb, Re2, Valgrind

Scripting Language

Julia, Lua, Nextflow, nim, Octave, Perl, Python, Qt, Qwt, R, Rstudio, Ruby, Scala, Tcl, Tk

Database

MongoDB, MySQL, Pgsql, RocksDB, Sqlite

Detailed list of software installed on Artemis, in alphabetical order

3D-Caffe

Software link to site

https://github.com/yulequan/3D-Caffe

Description

3D Caffe library for 3D classification or segmentation problem.

Version

1.0.0-rc3

Usage instructions

module load caffe-3d

Link to user guide/tutorial

https://github.com/yulequan/3D-Caffe

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Abaqus

Software link to site

https://www.3ds.com/products-services/simulia/products/abaqus/

Description

ABAQUS Finite Element Analysis products.

Version

6.14-1, 2016

Usage instructions

module load abaqus/2016 or module load abaqus/6.14-1

Link to user guide/tutorial

https://www.3ds.com/support/documentation/users-guides/

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Abricate

Software link to site

https://github.com/tseemann/abricate

Description

Mass screening of contigs for antibiotic resistance genes.

Version

0.3, 0.5, 0.7, 0.8

Usage instructions

module load abricate/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/tseemann/abricate

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Abyss

Software link to site

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Description

De novo genome sequence assembler.

Version

1.9.0

Usage instructions

module load abyss/1.9.0

Link to user guide/tutorial

https://github.com/bcgsc/abyss#abyss

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Abyss-mpi

Software link to site

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Description

De novo genome sequence assembler.

Version

1.9.0, 2.0.2

Usage instructions

module load abyss-mpi/1.9.0

Link to user guide/tutorial

https://github.com/bcgsc/abyss#abyss

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AdapterRemoval

Software link to site

https://github.com/MikkelSchubert/adapterremoval

Description

This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.

Version

2.2.2

Usage instructions

module load adapterremoval/2.2.2

Link to user guide/tutorial

https://github.com/MikkelSchubert/adapterremoval

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afni

Software link to site

https://afni.nimh.nih.gov/download

Description

AFNI (Analysis of Functional NeuroImages)

Version

17.2.02

Usage instructions

module load afni

Link to user guide/tutorial

https://afni.nimh.nih.gov/download

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AfterQC

Software link to site

https://github.com/OpenGene/AfterQC

Description

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

Version

0.9.6

Usage instructions

module load afterqc/0.9.6

Link to user guide/tutorial

https://github.com/OpenGene/AfterQC

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Ag

Software link to site

https://github.com/ggreer/the_silver_searcher

Description

A code searching tool similar to ack, with a focus on speed.

Version

2.1.0

Usage instructions

module load ag/2.1.0

Link to user guide/tutorial

https://github.com/ggreer/the_silver_searcher

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Aligngraph

Software link to site

https://github.com/baoe/AlignGraph

Description

Algorithm for secondary de novo genome assembly guided by closely related references.

Version

3242011

Usage instructions

module load aligngraph/3242011

Link to user guide/tutorial

https://github.com/baoe/AlignGraph

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AlleleSeq

Software link to site

http://alleleseq.gersteinlab.org/home.html

Description

AlleleSeq pipeline - ake a large collection of reads generated from ChIP-seq or RNA-seq experiments associated with an individual and detect single nucleotide variants

Version

1.2a

Usage instructions

module load alleleseq/1.2a

Link to user guide/tutorial

http://info.gersteinlab.org/AlleleSeq

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Allpathslg

Software link to site

http://software.broadinstitute.org/allpaths-lg/blog/

Description

The new short read genome assembler from the Computational Research and Development group at the Broad Institute.

Version

52488

Usage instructions

module load allpathslg/52488

Link to user guide/tutorial

ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/AllPaths-LG_Manual.pdf

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Amos

Software link to site

http://amos.sourceforge.net/wiki/index.php/AMOS

Description

A collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

Version

3.1.0

Usage instructions

module load amos/3.1.0

Link to user guide/tutorial

http://amos.sourceforge.net/wiki/index.php/AMOS_Getting_Started

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AmrPlusPlus

Software link to site

https://github.com/cdeanj/amrplusplus

Description

A high-throughput analysis pipeline to identify and characterize resistance genes from metagenomic sequence data

Version

0.0.0

Usage instructions

module load amrplusplus

Link to user guide/tutorial

https://github.com/cdeanj/amrplusplus

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Anaconda

Software link to site

https://www.anaconda.com/

Description

This is the Python 3.5.3 version of Anaconda. Anaconda is the leading open data science platform powered by Python.

Version

4.2.0

Usage instructions

module load anaconda/4.2.0

Link to user guide/tutorial

https://docs.anaconda.com

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Anaconda2

Software link to site

https://www.anaconda.com/

Description

This is the Python 2.7 version of Anaconda. Anaconda is the leading open data science platform powered by Python.

Version

5.0.1, 2019.03

Usage instructions

module load anaconda2/xxx (where xxx is the version)

Link to user guide/tutorial

https://docs.anaconda.com

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Ann

Software link to site

https://www.cs.umd.edu/~mount/ANN/

Description

ANN is a library written in C++, which supports data structures and algorithms for both exact and approximate nearest neighbor searching in arbitrarily high dimensions.

Version

1.1.2

Usage instructions

module load ann/1.1.2

Link to user guide/tutorial

https://www.cs.umd.edu/~mount/ANN/Files/1.1.2/ANNmanual_1.1.pdf

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AnnotSV

Software link to site

https://lbgi.fr/AnnotSV/

Description

Annotation and Ranking of Human Structural Variations

Version

2.1

Usage instructions

module load annotsv

Link to user guide/tutorial

https://lbgi.fr/AnnotSV/

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AnnotSV

Software link to site

https://lbgi.fr/AnnotSV/

Description

Annotation and Ranking of Human Structural Variations

Version

2.1

Usage instructions

module load annotsv

Link to user guide/tutorial

https://lbgi.fr/AnnotSV/

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Annovar

Software link to site

http://annovar.openbioinformatics.org/en/latest/

Description

A software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

Version

20150619, 20170716, 20180416

Usage instructions

module load annovar/xxx (wheree xxx is the version)

Link to user guide/tutorial

http://annovar.openbioinformatics.org/en/latest/

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ANSYS

Software link to site

http://www.ansys.com/

Description

An engineering simulation for general purpose finite element analysis and computational fluid dynamics.

Version

172, 180, 181, 182, 190, 191, 192, 193, 194, 2019R1, 2019R2

Usage instructions

module load ansys/xxx (where xxx is the version number)

Link to user guide/tutorial

http://www.ansys.com/Resource-Library

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AnsysEM

Software link to site

http://www.ansys.com/

Description

A unified platform for electromagnetic, circuit and system simulation.

Version

170, 181, 182, 193

Usage instructions

module load ansysEM/xxx (where xxx is the version number)

Link to user guide/tutorial

https://support.ansys.com/staticassets/ANSYS/Conference/Palm%20Beach/downloads/Introduction%20to%20ANSYS%20Electromagnetic%20Solutions.pdf

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Ant

Software link to site

http://ant.apache.org/

Description

A Java library and command-line tool that builds files as targets and extension points dependent upon each other.

Version

1.9.4, 1.10.3

Usage instructions

module load ant/xxx (where xxx is the version)

Link to user guide/tutorial

http://ant.apache.org/manual/index.html

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ANTs

Software link to site

http://stnava.github.io/ANTs/

Description

ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.

Version

2.2.0

Usage instructions

module load ants

Link to user guide/tutorial

https://github.com/stnava/ANTsDoc/raw/master/ants2.pdf

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Aragorn

Software link to site

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

Description

tRNA (and tmRNA) detection.

Version

1.2.36

Usage instructions

module load aragorn/1.2.36

Link to user guide/tutorial

http://mbio-serv2.mbioekol.lu.se/ARAGORN/

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Argtable2

Software link to site

http://argtable.sourceforge.net/

Description

An ANSI C library for parsing GNU style command line arguments

Version

13

Usage instructions

module load argtable2

Link to user guide/tutorial

http://argtable.sourceforge.net/doc/argtable2-intro.html

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Aria2

Software link to site

https://aria2.github.io/

Description

A fast download utility.

Version

1.25.0

Usage instructions

module load aria2/1.25.0

Link to user guide/tutorial

https://aria2.github.io/manual/en/html/index.html

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Armadillo

Software link to site

http://arma.sourceforge.net/

Description

Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

Version

8.500.0

Usage instructions

module load armadillo/8.500.0

Link to user guide/tutorial

http://arma.sourceforge.net/docs.html

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armatus

Software link to site

https://github.com/kingsfordgroup/armatus

Description

Multiresolution domain calling software for chromosome conformation capture interaction matricies.

Version

2.2

Usage instructions

module load armatus

Link to user guide/tutorial

https://github.com/kingsfordgroup/armatus/blob/master/README.md

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Arpack-Ng

Software link to site

https://github.com/opencollab/arpack-ng

Description

None

Version

3.1.5

Usage instructions

module load arpack-ng/3.1.5

Link to user guide/tutorial

https://github.com/opencollab/arpack-ng/tree/master/DOCUMENTS

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Artemis

Software link to site

https://www.sanger.ac.uk/science/tools/artemis

Description

A genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

Version

17

Usage instructions

module load artemis

Link to user guide/tutorial

https://www.sanger.ac.uk/science/tools/artemis

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ArtificialFastqGenerator

Software link to site

https://sourceforge.net/projects/artfastqgen/

Description

ArtificialFastqGenerator takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format

Version

19_05_2015

Usage instructions

module load artfastgen

Link to user guide/tutorial

https://sourceforge.net/p/artfastqgen/wiki/Home/

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ASHS

Software link to site

https://sites.google.com/site/hipposubfields/home

Description

Automatic Segmentation of Hippocampal Subfields (ASHS)

Version

20170223

Usage instructions

module load ashs

Link to user guide/tutorial

https://sites.google.com/site/hipposubfields/tutorial

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Atlas

Software link to site

http://math-atlas.sourceforge.net/

Description

Automatically Tuned Linear Algebra Software.

Version

3.10.2, 3.10.3

Usage instructions

module load atlas/3.10.2 or module load atlas 3.10.3

Link to user guide/tutorial

http://math-atlas.sourceforge.net/faq.html#help

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Augustus

Software link to site

http://bioinf.uni-greifswald.de/augustus/

Description

A gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie Knig and Lizzy Gerischer. It can be used as an ab initio program, which means it bases its prediction purely on the sequence.

Version

3.2.1, 3.3

Usage instructions

module load augustus/3.2.1 or module load augustus/3.3

Link to user guide/tutorial

http://bioinf.uni-greifswald.de/augustus/

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Autoconf

Software link to site

https://www.gnu.org/software/autoconf/autoconf.html

Description

An extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.

Version

2.69

Usage instructions

module load autoconf/2.69

Link to user guide/tutorial

https://www.gnu.org/software/autoconf/autoconf.html#documentation

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Automake

Software link to site

https://www.gnu.org/software/automake/

Description

A tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Automake requires the use of Autoconf.

Version

1.14, 1.15

Usage instructions

module load automake/1.14 or module load automake/1.15

Link to user guide/tutorial

https://www.gnu.org/software/automake/#documentation

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bam-readcount

Software link to site

https://github.com/genome/bam-readcount/

Description

count DNA sequence reads in BAM files

Version

0.8.0

Usage instructions

module load bam-readcount

Link to user guide/tutorial

https://github.com/genome/bam-readcount/

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Bambamc

Software link to site

https://github.com/gt1/bambamc

Description

This package contains mainly a lightweight C implementation of the read name collation code from the larger libmaus

Version

0.0.50

Usage instructions

module load bambamc/0.0.50

Link to user guide/tutorial

https://github.com/gt1/bambamc

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Bamtools

Software link to site

https://github.com/pezmaster31/bamtools

Description

BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

Version

2.4.0

Usage instructions

module load bamtools/2.4.0

Link to user guide/tutorial

https://github.com/pezmaster31/bamtools/wiki

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bamUtil

Software link to site

https://github.com/statgen/bamUtil

Description

Programs for working on SAM/BAM files.

Version

1.0.14

Usage instructions

module load bamutil/1.0.14

Link to user guide/tutorial

https://genome.sph.umich.edu/wiki/BamUtil

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Baps

Software link to site

http://www.helsinki.fi/bsg/software/BAPS/

Description

Bayesian Analysis of Population Structure.

Version

6

Usage instructions

module load baps/6

Link to user guide/tutorial

http://www.helsinki.fi/bsg/software/BAPS/macSnow/BAPS6manual.pdf

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barrnap

Software link to site

https://github.com/tseemann/barrnap

Description

Barrnap predicts the location of ribosomal RNA genes in genomes.

Version

0.6

Usage instructions

module load barrnap

Link to user guide/tutorial

https://github.com/tseemann/barrnap

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BASE

Software link to site

https://github.com/dhlbh/BASE

Description

A fast and accurate de novo genome assembler for longer NGS reads

Version

1.0

Usage instructions

module load base/1.0

Link to user guide/tutorial

https://github.com/dhlbh/BASE/blob/master/src/Howto.txt

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Basespace

Software link to site

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub.html

Description

BaseSpace Sequence Hub Command Line Interface

Version

0.8.1, 0.9.11.631, 0.10.8

Usage instructions

module load basespace/0.8.1 or module load basespace/0.9.11.631

Link to user guide/tutorial

https://support.illumina.com/

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BatMeth

Software link to site

https://code.google.com/archive/p/batmeth/

Description

Improved mapper for bisulfite sequencing reads on DNA methylation

Version

1.04b

Usage instructions

module load batmeth/1.04b

Link to user guide/tutorial

https://code.google.com/archive/p/batmeth/wikis

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BayesAss

Software link to site

http://www.rannala.org/inference-of-recent-migration/

Description

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

Version

3.0.4

Usage instructions

module load bayesass

Link to user guide/tutorial

https://sourceforge.net/projects/bayesass/files/BA3/3.0.4/docs/BA3Manual.pdf/download

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Bazel

Software link to site

https://bazel.build/

Description

Bazel is a tool that automates software builds and tests.

Version

0.2.3, 0.3.2, 0.4.3, 0.4.5, 0.5.1, 0.7.0, 0.11.0, 0.16.1, 0.21.0, 0.25.2, 0.28.0

Usage instructions

module load bazel/xxx (where xxx represents the version number)

Link to user guide/tutorial

https://docs.bazel.build/

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Bbmap

Software link to site

https://sourceforge.net/projects/bbmap/

Description

BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.

Version

36.92, 37.98

Usage instructions

module load bbmap/36.92 or module load bbmap/37.98

Link to user guide/tutorial

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/

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BCFtools

Software link to site

https://samtools.github.io/bcftools/bcftools.html

Description

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.

Version

1.1-intel, 1.2, 1.3.1, 1.3.1-intel, 1.5, 1.5-intel, 1.6, 1.6-intel, 1.8, 1.9, 1.9-102

Usage instructions

module load bcftools/xxx (where xxx represents the version number)

Link to user guide/tutorial

https://samtools.github.io/bcftools/bcftools.html

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Bcl2fastq

Software link to site

https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html

Description

bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.

Version

2.19

Usage instructions

module load bcl2fastq2

Link to user guide/tutorial

https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/documentation.html

Special licensing notes

Required for supernova

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Beagle

Software link to site

https://github.com/beagle-dev/beagle-lib

Description

A general purpose library for evaluating the likelihood of sequence evolution on trees.

Version

20150401

Usage instructions

module load beagle/20150401

Link to user guide/tutorial

https://github.com/beagle-dev/beagle-lib/wiki

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Beast

Software link to site

http://beast.bio.ed.ac.uk/

Description

Bayesian Evolutionary Analysis by Sampling Trees.

Version

1.8.2, 2.2.0, 2.3.1, 2.4.2

Usage instructions

module load beast/xxx (where xxx represents the version number)

Link to user guide/tutorial

http://beast.bio.ed.ac.uk/home#toc-4

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BEDOPS

Software link to site

https://bedops.readthedocs.io/en/latest/

Description

BEDOPS high-performance genomic feature operations

Version

2.4.30

Usage instructions

module load bedops/2.4.30

Link to user guide/tutorial

https://bedops.readthedocs.io/en/latest/

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Bedtools

Software link to site

http://bedtools.readthedocs.io/en/latest/

Description

The bedtools utilities are a swiss-army knife of tools for a wide range of genomics arithmetic and analysis tasks.

Version

2.24.0, 2.25.0, 2.26.0

Usage instructions

module load bedtools/xxx (where xxx represents the version number)

Link to user guide/tutorial

http://bedtools.readthedocs.io/en/latest/content/general-usage.html

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Binutils

Software link to site

https://www.gnu.org/software/binutils/

Description

GNU Binary file utilities.

Version

2.26, 2.30

Usage instructions

module load binutils/2.26 or module load binutils/2.30

Link to user guide/tutorial

https://sourceware.org/binutils/docs-2.30/

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biobambam2

Software link to site

https://github.com/gt1/biobambam2

Description

Tools for early stage alignment file processing

Version

2.0.72

Usage instructions

module load biobambam2

Link to user guide/tutorial

https://github.com/gt1/biobambam2

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Biogeme

Software link to site

http://biogeme.epfl.ch/home.html

Description

Biogeme is an open source freeware designed for the maximum likelihood estimation of parametric models in general, with a special emphasis on discrete choice models.

Version

2.5

Usage instructions

module load biogeme/2.26

Link to user guide/tutorial

http://biogeme.epfl.ch/pdfdocuments.html

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Biopieces

Software link to site

https://github.com/maasha/biopieces

Description

Biopieces is a bioinformatic framework of tools easily used and easily created.

Version

1

Usage instructions

module load biopieces/1

Link to user guide/tutorial

https://github.com/maasha/biopieces

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Bismark

Software link to site

https://github.com/FelixKrueger/Bismark

Description

A tool to map bisulfite converted sequence reads and determine cytosine methylation states.

Version

0.18.2, 0.19.0, 0.20.0, 0.22.1

Usage instructions

module load bismark/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/FelixKrueger/Bismark/tree/master/Docs

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Bison

Software link to site

https://www.gnu.org/software/bison/

Description

None

Version

3

Usage instructions

module load bison/3

Link to user guide/tutorial

https://www.gnu.org/software/bison/manual/

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Blas

Software link to site

http://www.netlib.org/blas/

Description

None

Version

3.5.0

Usage instructions

module load blas/3.5.0

Link to user guide/tutorial

http://www.netlib.org/blas/#_documentation

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Blasr

Software link to site

https://github.com/PacificBiosciences/blasr

Description

The PacBio long read aligner

Version

1.3.1

Usage instructions

module load blasr/1.3.1

Link to user guide/tutorial

https://github.com/PacificBiosciences/blasr/wiki

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Blast

Software link to site

https://blast.ncbi.nlm.nih.gov/Blast.cgi

Description

NCBI Basic Local Alignment Search Tool for DNA sequences.

Version

2.2.26, 2.2.30

Usage instructions

module load blast/2.2.26 or module load blast/2.2.30

Link to user guide/tutorial

ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html

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BLAST+

Software link to site

https://www.ncbi.nlm.nih.gov/books/NBK279671/

Description

BLAST+ is a suite of command-line tools to run BLAST.

Version

2.3.0, 2.4.0, 2.6.0, 2.7.1

Usage instructions

module load blast+/xxx (where xxx is the version number)

Link to user guide/tutorial

https://www.ncbi.nlm.nih.gov/books/NBK279671/

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Blat

Software link to site

https://genome.ucsc.edu/FAQ/FAQblat.html

Description

Web tools to help understand the human genome.

Version

3.6

Usage instructions

module load blat/3.6

Link to user guide/tutorial

https://genome.ucsc.edu/goldenPath/help/blatSpec.html

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BlobTools

Software link to site

https://github.com/DRL/blobtools

Description

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

Version

1.0

Usage instructions

module load blobtools

Link to user guide/tutorial

https://github.com/DRL/blobtools

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Boost

Software link to site

http://www.boost.org/

Description

Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.

Version

1.55.0, 1.57.0, 1.59.0, 1.61.0, 1.62.0, 1.64.0, 1.66.0, 1.67.0

Usage instructions

module load boost/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.boost.org/doc/

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Bowtie

Software link to site

http://bowtie-bio.sourceforge.net/index.shtml

Description

Bowtieis an ultrafast, memory-efficient short read aligner.

Version

1.1.1, 1.1.2

Usage instructions

module load bowtie/1.1.1 or module load bowtie/1.1.2

Link to user guide/tutorial

http://bowtie-bio.sourceforge.net/manual.shtml

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Bowtie2

Software link to site

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Description

Bowtieis an ultrafast, memory-efficient short read aligner.

Version

2.2.5, 2.3.3.1

Usage instructions

module load bowtie2/2.2.5 or module load bowtie2/2.3.3.1

Link to user guide/tutorial

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

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bpp

Software link to site

http://abacus.gene.ucl.ac.uk/software.html

Description

Bayesian analysis of genomic sequence data under the multispecies coalescent model.

Version

3.3a

Usage instructions

module load bpp/3.3a

Link to user guide/tutorial

http://abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf

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Bracken

Software link to site

https://ccb.jhu.edu/software/bracken/

Description

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

Version

1.0.0

Usage instructions

module load bracken/1.0.0

Link to user guide/tutorial

https://ccb.jhu.edu/software/bracken/index.shtml?t=manual

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BRAKER1

Software link to site

http://topaz.gatech.edu/Genemark/braker1.html

Description

BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

Version

1.9

Usage instructions

module load braker1

Link to user guide/tutorial

http://topaz.gatech.edu/Genemark/braker1.html

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BRAKER2

Software link to site

http://topaz.gatech.edu/Genemark/braker1.html

Description

Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS

Version

2, 2.0.6

Usage instructions

module load braker2/2.0 or module load braker2/2.0.6

Link to user guide/tutorial

http://topaz.gatech.edu/Genemark/braker1.html

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Brig

Software link to site

http://brig.sourceforge.net/

Description

BRIG can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

Version

0.95

Usage instructions

module load brig/0.95

Link to user guide/tutorial

https://sourceforge.net/projects/brig/files/

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Busco

Software link to site

http://busco.ezlab.org/

Description

BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB (www.orthodb.org) to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.

Version

1.1b, 2.0, 3.0, 3.0.2

Usage instructions

module load busco/xxx (where xxx is the version number)

Link to user guide/tutorial

http://gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf

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Bvatools

Software link to site

https://bitbucket.org/mugqic/bvatools

Description

Bam and Variant Analysis Tools.

Version

1.6

Usage instructions

module load bvatools/1.6

Link to user guide/tutorial

https://bitbucket.org/mugqic/bvatools/overview

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BWA

Software link to site

http://bio-bwa.sourceforge.net/

Description

BWA is a software package for mapping low divergent sequences against a large reference genome, such as the human genome.

Version

0.6.1, 0.7.12, 0.7.15, 0.7.15-intel, 0.7.16a, 0.7.17

Usage instructions

module load bwa/xxx (where xxx represents the version number)

Link to user guide/tutorial

http://bio-bwa.sourceforge.net/bwa.shtml

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bzip2

Software link to site

http://www.bzip.org/

Description

None

Version

1.0.6

Usage instructions

module load bzip2/1.0.6

Link to user guide/tutorial

http://www.bzip.org/docs.html

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c3d

Software link to site

https://sourceforge.net/projects/c3d/

Description

Convert3D Medical Image Processing Tool

Version

1.0.0

Usage instructions

module load c3d

Link to user guide/tutorial

https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md

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CAFExp

Software link to site

https://github.com/hahnlab/CAFExp

Description

Software for Computational Analysis of gene Family Evolution

Version

5

Usage instructions

module load cafexp

Link to user guide/tutorial

https://github.com/hahnlab/CAFExp

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Caffe

Software link to site

http://caffe.berkeleyvision.org/

Description

Caffe is a deep learning framework.

Version

1.0.0-rc3, 1.0.0

Usage instructions

module load caffe/1.0.0-rc3 or module load caffe/1.0.0

Link to user guide/tutorial

http://caffe.berkeleyvision.org/

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Caffe2

Software link to site

https://caffe2.ai/

Description

A New Lightweight, Modular, and Scalable Deep Learning Framework

Version

0.8.1

Usage instructions

module load caffe2

Link to user guide/tutorial

https://caffe2.ai/docs/tutorials.html

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Cairo

Software link to site

https://cairographics.org/

Description

None

Version

1.12.18, 1.14.10

Usage instructions

module load cairo/1.12.18 or module load cairo/1.14.10

Link to user guide/tutorial

https://cairographics.org/documentation/

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cairomm

Software link to site

https://www.cairographics.org/cairomm/

Description

cairomm is a C++ wrapper for the cairo graphics library

Version

1.15.3

Usage instructions

module load cairomm

Link to user guide/tutorial

https://www.cairographics.org/cairomm/

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camino

Software link to site

http://camino.cs.ucl.ac.uk/

Description

Camino is an open-source software toolkit for diffusion MRI processing.

Version

a844005b39c2fc7fd5d33c6af977e44248de42cd

Usage instructions

module load camino

Link to user guide/tutorial

http://camino.cs.ucl.ac.uk/index.php?n=Main.Tutorials

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Canu

Software link to site

http://canu.readthedocs.io/en/latest/

Description

A single molecule sequence assembler for genomes large and small.

Version

1.3, 1.6, 1.7, 1.8, 1.8+268

Usage instructions

module load canu/xxx (where xxx is the version number)

Link to user guide/tutorial

http://canu.readthedocs.io/en/latest/tutorial.html

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Cap3

Software link to site

http://seq.cs.iastate.edu/cap3.html

Description

CAP3 Sequence Assembly Program.

Version

20150421

Usage instructions

module load cap3/20150421

Link to user guide/tutorial

http://seq.cs.iastate.edu/cap3.html

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Cblas

Software link to site

https://software.intel.com/en-us/node/520728

Description

None

Version

3.5.0

Usage instructions

module load cblas/3.5.0

Link to user guide/tutorial

https://software.intel.com/en-us/node/520728

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CCMetagen

Software link to site

https://github.com/vrmarcelino/CCMetagen

Description

Microbiome classification pipeline

Version

0.1, 1.1.3

Usage instructions

module load ccmetagen/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/vrmarcelino/CCMetagen

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Cd-Hit

Software link to site

http://weizhongli-lab.org/cd-hit/

Description

A program for clustering and comparing protein or nucleotide sequences.

Version

4.6.1, 4.6.5

Usage instructions

module load cd-hit/4.6.1

Link to user guide/tutorial

http://weizhongli-lab.org/lab-wiki/doku.php?id=cd-hit-user-guide

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Cddlib

Software link to site

https://www.inf.ethz.ch/personal/fukudak/cdd_home/

Description

The C-library cddlib is a C implementation of the Double Description
Method of Motzkin et al. for generating all vertices (i.e. extreme points)
and extreme rays of a general convex polyhedron

Version

094h

Usage instructions

module load cddlib

Link to user guide/tutorial

ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlibman/cddlibman.html

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Cell Ranger

Software link to site

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Description

A set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell gene counting

Version

3.0.2

Usage instructions

module load cellranger

Link to user guide/tutorial

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

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Centrifuge

Software link to site

http://www.ccb.jhu.edu/software/centrifuge

Description

Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labelling of reads and quantification of species.

Version

1.0.3-beta, 1.0.4-beta

Usage instructions

module load centrifuge/1.0.3-beta

Link to user guide/tutorial

http://www.ccb.jhu.edu/software/centrifuge/manual.shtml

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CFITSIO

Software link to site

https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html

Description

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

Version

3.4.10, 3.41

Usage instructions

module load cfitsio/xxx (where xxx is the version)

Link to user guide/tutorial

https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html

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CGAL

Software link to site

http://www.cgal.org/

Description

A collaborative effort to develop a robust, easy to use, and efficient C++ software library of geometric data structures and algorithms.

Version

4.5.1, 4.7, 4.9, 4.10, 4.11

Usage instructions

module load cgal/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.cgal.org/documentation.html

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CGNS

Software link to site

https://cgns.github.io/

Description

The CFD General Notation System (CGNS) provides a general, portable, and extensible standard for the storage and retrieval of computational fluid dynamics (CFD) analysis data.

Version

3.2.1

Usage instructions

module load cgns/3.2.1

Link to user guide/tutorial

https://cgns.github.io/CGNS_docs_current/index.html

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Chimera

Software link to site

https://www.cgl.ucsf.edu/chimera/

Description

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.

Version

1.11

Usage instructions

module load chimera/1.11

Link to user guide/tutorial

https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/

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Chimeraslayer

Software link to site

http://microbiomeutil.sourceforge.net/

Description

ChimeraSlayer is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

Version

20110519

Usage instructions

module load chimeraslayer/20110519

Link to user guide/tutorial

http://microbiomeutil.sourceforge.net/

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ChunkChromosome

Software link to site

https://genome.sph.umich.edu/wiki/ChunkChromosome

Description

ChunkChromosome is a helper utility for minimac and MaCH.

Version

27-05-14

Usage instructions

module load chunkchromosome

Link to user guide/tutorial

https://genome.sph.umich.edu/wiki/ChunkChromosome

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Circos

Software link to site

http://circos.ca/software/

Description

Flexible and automatable circular data visualisation.

Version

0.69-3

Usage instructions

module load circos/0.69-3

Link to user guide/tutorial

http://circos.ca/documentation/

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Clhep

Software link to site

http://proj-clhep.web.cern.ch/proj-clhep/

Description

A Class Library for High Energy Physics.

Version

2.1.1.0, 2.2.0.8, 2.3.1.1

Usage instructions

module load clhep/xxx (where xxx represents the version number)

Link to user guide/tutorial

http://proj-clhep.web.cern.ch/proj-clhep/index.html#docu

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ClinSV

Software link to site

https://github.com/KCCG/ClinSV

Description

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data

Version

0.9

Usage instructions

module load clinsv/0.9

Link to user guide/tutorial

https://github.com/KCCG/ClinSV

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Clonalframeml

Software link to site

https://github.com/xavierdidelot/ClonalFrameML

Description

Efficient inference of recombination in bacterial genomes.

Version

1

Usage instructions

module load clonalframeml/1

Link to user guide/tutorial

https://github.com/xavierdidelot/ClonalFrameML/wiki

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Clustal Omega

Software link to site

http://www.clustal.org/omega/

Description

Multiple alignment of nucleic acid and protein sequences

Version

1.2.4

Usage instructions

module load clustal-omega

Link to user guide/tutorial

http://www.clustal.org/omega/

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Clustal W/X

Software link to site

http://www.clustal.org/clustal2/

Description

Multiple alignment of nucleic acid and protein sequences

Version

2.1

Usage instructions

module load clustal

Link to user guide/tutorial

http://www.clustal.org/clustal2/

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Cmake

Software link to site

https://cmake.org/

Description

Cross-platform, open-source build system.

Version

3.0.1, 3.4.0, 3.9.4, 3.11.4, 3.13.4

Usage instructions

module load cmake/xxx (where xxx represents the version number)

Link to user guide/tutorial

https://cmake.org/documentation/

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CNVnator

Software link to site

https://github.com/abyzovlab/CNVnator

Description

A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

Version

0.4

Usage instructions

module load cnvnator

Link to user guide/tutorial

https://github.com/abyzovlab/CNVnator

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Codonphyml

Software link to site

https://sourceforge.net/projects/codonphyml/

Description

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction.

Version

dev_1.00_201407.24, 20150402

Usage instructions

module load codonphyml/dev_1.00_201407.24 or module load codonphyml/20150402

Link to user guide/tutorial

https://sourceforge.net/p/codonphyml/wiki/Home/

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coevol

Software link to site

https://github.com/bayesiancook/coevol

Description

Correlated evolution of substitution rates and quantitative traits

Version

1.5

Usage instructions

module load coevol/1.5

Link to user guide/tutorial

https://github.com/bayesiancook/coevol

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Conn

Software link to site

https://www.nitrc.org/projects/conn/

Description

CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).

Version

15g, 17a

Usage instructions

module load conn/15g or module load conn/17a

Link to user guide/tutorial

https://www.nitrc.org/frs/download.php/9356/CONN_fMRI_Functional_connectivity_toolbox_manual_v17.pdf

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Cortex

Software link to site

http://cortexassembler.sourceforge.net/

Description

An efficient and low-memory software framework for analysis of genomes using sequence data.

Version

1.0.5.21

Usage instructions

module load cortex/1.0.5.21

Link to user guide/tutorial

http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf

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Crest

Software link to site

http://www.stjuderesearch.org/site/lab/zhang

Description

CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data.

Version

0.01

Usage instructions

module load crest/0.01

Link to user guide/tutorial

http://www.stjuderesearch.org/site/lab/zhang

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Cuda

Software link to site

http://www.nvidia.com/object/cuda_home_new.html

Description

CUDA is NVIDIA's parallel computing architecture.

Version

6.0.37, 6.5.14-test, 6.5.14, 7.5.18, 8.0.44, 9.0.176, 9.1.85, 9.2.148, 10.0.130, 10.1.105

Usage instructions

module load cuda/xxx (where xxx represents version number)

Link to user guide/tutorial

https://devtalk.nvidia.com/

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Cuda2

Software link to site

https://developer.nvidia.com/cuda-toolkit-20-august-2008

Description

CUDA is NVIDIA's parallel computing architecture.

Version

6.0.37, 6.5.14-test,6.5.14, 7.5.18

Usage instructions

module load cuda2/6.0.37

Link to user guide/tutorial

https://developer.nvidia.com/cuda-toolkit-20-august-2008

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Cufflinks

Software link to site

https://github.com/cole-trapnell-lab/cufflinks

Description

Transcriptome assembly and differential expression analysis for RNA-Seq.

Version

2.2.1

Usage instructions

module load cufflinks/2.2.1

Link to user guide/tutorial

https://github.com/cole-trapnell-lab/cufflinks/tree/master/doc

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curl

Software link to site

https://curl.haxx.se/

Description

curl is used in command lines or scripts to transfer data.

Version

7.59.0

Usage instructions

module load curl/7.59.0

Link to user guide/tutorial

https://curl.haxx.se/docs/

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Cutadapt

Software link to site

http://cutadapt.readthedocs.io/en/stable/index.html

Description

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Version

1.8.3

Usage instructions

module load cutadapt/1.8.3

Link to user guide/tutorial

https://cutadapt.readthedocs.io/en/stable/

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Cyberduck

Software link to site

https://duck.sh/

Description

Cyberduck CLI program "duck"

Version

0.6.2

Usage instructions

module load cyberduck/0.6.2. Can upload directly to AARNet CloudStor from Artemis HPC. Use a CloudStor App password instead of your UniKey Password.

Link to user guide/tutorial

https://support.aarnet.edu.au/hc/en-us/articles/115007168507-Can-I-use-the-command-line-or-WebDav-

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Dbus

Software link to site

https://www.freedesktop.org/wiki/Software/dbus/

Description

None

Version

1.8.16

Usage instructions

module load dbus/1.8.16

Link to user guide/tutorial

https://www.freedesktop.org/wiki/Software/dbus/#index4h1

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Dbus-Glib

Software link to site

https://dbus.freedesktop.org/doc/dbus-glib/

Description

None

Version

0.104

Usage instructions

module load dbus-glib/0.104

Link to user guide/tutorial

https://dbus.freedesktop.org/doc/dbus-glib/

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dcm2niix

Software link to site

https://github.com/rordenlab/dcm2niix

Description

dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.

Version

1.0.20170624

Usage instructions

module load dcm2niix

Link to user guide/tutorial

https://github.com/rordenlab/dcm2niix

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Dcmtk

Software link to site

http://dicom.offis.de/dcmtk.php.en

Description

DCMTK is a collection of libraries and applications implementing large parts the DICOM standard.

Version

3.6.1

Usage instructions

module load dcmtk/3.6.1

Link to user guide/tutorial

http://support.dcmtk.org/redmine/projects/dcmtk/wiki

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Delly

Software link to site

https://github.com/dellytools/delly

Description

Delly is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

Version

0.6.7, 0.7.6, 0.7.8, 0.7.9

Usage instructions

module load delly/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/dellytools/delly

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DETONATE

Software link to site

http://deweylab.biostat.wisc.edu/detonate/

Description

DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

Version

1.11

Usage instructions

module load detonate/1.11

Link to user guide/tutorial

http://deweylab.biostat.wisc.edu/detonate/

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Diamond

Software link to site

https://github.com/bbuchfink/diamond

Description

Accelerated BLAST compatible local sequence aligner.

Version

0.8.28.90, 0.9.10

Usage instructions

module load diamond/0.8.28.90

Link to user guide/tutorial

https://github.com/bbuchfink/diamond/wiki

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Dlpoly

Software link to site

https://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic

Description

General purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory.

Version

4.07

Usage instructions

module load dlpoly/4.07

Link to user guide/tutorial

ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMAN4.pdf

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Doxygen

Software link to site

http://www.stack.nl/~dimitri/doxygen/

Description

A documentation system for various programming languages.

Version

1.8.6, 1.8.9.1

Usage instructions

module load doxygen/1.8.6 or module load doxygen/1.8.9.1

Link to user guide/tutorial

http://www.stack.nl/~dimitri/doxygen/manual/index.html

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Drive5

Software link to site

http://www.drive5.com/

Description

drive5 collection of Python scripts provided to assist in processing data for UPARSE and other multi-step pipelines.

Version

0

Usage instructions

module load drive5/0

Link to user guide/tutorial

http://www.drive5.com/

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DTI-TK

Software link to site

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php

Description

DTI-TK is a spatial normalization and atlas construction toolkit optimised for examining white matter morphometry using DTI data.

Version

2.3.1

Usage instructions

module load dtitk/2.3.1

Link to user guide/tutorial

http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.HomePage1

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dx-toolkit

Software link to site

https://github.com/dnanexus/dx-toolkit

Description

The DNAnexus Platform SDK

Version

0.276.0

Usage instructions

module load dx-toolkit

Link to user guide/tutorial

http://autodoc.dnanexus.com/

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Ea-Utils

Software link to site

https://expressionanalysis.github.io/ea-utils/

Description

ea-utils are command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.

Version

1.1.2-537

Usage instructions

module load ea-utils/1.1.2-537

Link to user guide/tutorial

https://expressionanalysis.github.io/ea-utils/

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Ec2-Api-Tools

Software link to site

http://docs.aws.amazon.com/cli/latest/userguide/installing.html

Description

Amazon Elastic Compute Cloud tools.

Version

1.7.5.1

Usage instructions

module load ec2-api-tools/1.7.5.1

Link to user guide/tutorial

http://docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.html

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EDirect

Software link to site

https://www.ncbi.nlm.nih.gov/books/NBK179288/

Description

Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.

Version

20150625, 8.60

Usage instructions

module load edirect/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.ncbi.nlm.nih.gov/books/NBK179288/#chapter6.Getting_Started

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EffectorP

Software link to site

http://effectorp.csiro.au/

Description

Fungal effector prediction in secretomes

Version

2.0

Usage instructions

module load effectorp

Link to user guide/tutorial

http://effectorp.csiro.au/instructions.html

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Eigen

Software link to site

http://eigen.tuxfamily.org/index.php

Description

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.

Version

3.2.4, 3.2.8

Usage instructions

module load eigen/3.2.4 or module load eigen/3.2.8

Link to user guide/tutorial

http://eigen.tuxfamily.org/index.php?title=Main_Page#Documentation

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Eigenvalue SoLvers for Petaflop-Applications (ELPA)

Software link to site

https://elpa.mpcdf.mpg.de/

Description

The publicly available ELPA library provides highly efficient and highly scalable direct eigensolvers for symmetric matrices.

Version

2016.05.001, 2018.05.001

Usage instructions

module load elpa/xxx (where xxx is the version number)

Link to user guide/tutorial

https://elpa.mpcdf.mpg.de/documentation

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emacs

Software link to site

https://www.gnu.org/software/emacs/

Description

An extensible and customisable text editor

Version

7.59.0

Usage instructions

module load curl/7.59.0

Link to user guide/tutorial

https://www.gnu.org/software/emacs/documentation.html

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Emboss

Software link to site

http://emboss.sourceforge.net/

Description

EMBOSS: The European Molecular Biology Open Software Suite.

Version

6.6.0

Usage instructions

module load emboss/6.6.0

Link to user guide/tutorial

http://emboss.sourceforge.net/support/

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EMMAX

Software link to site

http://genetics.cs.ucla.edu/emmax/

Description

EMMAX is a statistical test for large scale human or model organism association mapping accounting for the sample structure.

Version

20120210

Usage instructions

module load emmax/20120210

Link to user guide/tutorial

http://genetics.cs.ucla.edu/emmax/install.html

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EPA-ng

Software link to site

https://github.com/Pbdas/epa-ng

Description

Massively parallel phylogenetic placement of genetic sequences

Version

0.2.1-beta

Usage instructions

module load epa-ng

Link to user guide/tutorial

https://github.com/Pbdas/epa-ng

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Epacts

Software link to site

http://genome.sph.umich.edu/wiki/EPACTS

Description

EPACTS(Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data.

Version

3.3.2

Usage instructions

module load epacts/3.3.2

Link to user guide/tutorial

http://genome.sph.umich.edu/wiki/EPACTS#Getting_Started_With_Examples

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Epimine

Software link to site

https://sourceforge.net/projects/epimine/

Description

None

Version

2.25_v1.01, 2.16_2.17_v1.01, py3

Usage instructions

module load epimine/xxx (where xxx represents

Link to user guide/tutorial

https://sourceforge.net/p/epimine/wiki/Home/

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EVidenceModeler

Software link to site

https://github.com/EVidenceModeler/EVidenceModeler/releases

Description

The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.

Version

v1.1.1

Usage instructions

module load evidencemodeler

Link to user guide/tutorial

https://evidencemodeler.github.io/

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ExaBayes

Software link to site

https://sco.h-its.org/exelixis/web/software/exabayes/

Description

Exabayes is a software package for Bayesian tree inference.

Version

1.5

Usage instructions

module load exabayes/1.5

Link to user guide/tutorial

https://sco.h-its.org/exelixis/web/software/exabayes/manual/index.html

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EXCAVATOR2tool

Software link to site

https://sourceforge.net/projects/excavator2tool/files/latest/download

Description

EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs.

Version

1.1.2

Usage instructions

module load excavator2tool/1.1.2

Link to user guide/tutorial

https://sourceforge.net/projects/excavator2tool/files/EXCAVATOR2Manual.pdf/download

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Exciting

Software link to site

http://exciting-code.org/

Description

Exciting is a full-potential all-electron density-functional-theory package implementing the families of linearized augmented planewave methods.

Version

1

Usage instructions

module load exciting

Link to user guide/tutorial

http://exciting-code.org/documentation

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exonerate

Software link to site

http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Description

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

Version

2.2.0_x86_64

Usage instructions

module load exonerate

Link to user guide/tutorial

http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-user-guide

Special licensing notes

GPL

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Expat

Software link to site

http://expat.sourceforge.net/

Description

None

Version

2.1.0

Usage instructions

module load expat/2.1.0

Link to user guide/tutorial

http://www.xml.com/pub/1999/09/expat/index.html

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Falcon

Software link to site

https://github.com/PacificBiosciences/FALCON

Description

FALCON: experimental PacBio diploid assembler

Version

0.1, 0.5

Usage instructions

module load falcon/0.1 or module load falcon/0.5

Link to user guide/tutorial

https://github.com/PacificBiosciences/FALCON/wiki

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Falcon-Unzip

Software link to site

https://github.com/PacificBiosciences/FALCON

Description

FALCON-Unzip contains the modules that works with FALCON for full diploid assembly.

Version

52016

Usage instructions

module load falcon-unzip/52016

Link to user guide/tutorial

https://github.com/PacificBiosciences/FALCON/wiki

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FastME

Software link to site

http://www.atgc-montpellier.fr/fastme/

Description

Comprehensive, accurate and fast distance-based phylogeny inference program

Version

2.1.5

Usage instructions

module load fastme

Link to user guide/tutorial

http://www.atgc-montpellier.fr/fastme/usersguide.php

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Fastml

Software link to site

http://fastml.tau.ac.il/

Description

The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences.

Version

3.1, 3.1-b

Usage instructions

module load fastml/3.1 or module load fastml/3.1-b

Link to user guide/tutorial

http://fastml.tau.ac.il/

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fastp

Software link to site

https://github.com/OpenGene/fastp

Description

A tool designed to provide fast all-in-one preprocessing for FastQ files.

Version

0.19.6

Usage instructions

module load fastp/0.19.6

Link to user guide/tutorial

https://github.com/OpenGene/fastp

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fastPHASE

Software link to site

http://scheet.org/software.html

Description

fastPHASE is a program to estimate missing genotypes and unobserved haplotypes.

Version

1.4.8

Usage instructions

module load fastphase

Link to user guide/tutorial

http://scheet.org/code/fastphase_doc_1.4.pdf

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FastQC

Software link to site

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Description

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

Version

0.11.3, 0.11.7

Usage instructions

module load fastqc/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/

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fastQValidator

Software link to site

https://github.com/statgen/fastQValidator

Description

The fastQValidator validates the format of fastq files.

Version

0.1.1a

Usage instructions

module load fastqvalidator/0.1.1a

Link to user guide/tutorial

https://genome.sph.umich.edu/wiki/FastQValidator

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Fasttree

Software link to site

http://www.microbesonline.org/fasttree/

Description

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.

Version

2.1.8, 2.1.9, 2.1.10

Usage instructions

module load fasttree/2.1.8 or module load fasttree/2.1.9

Link to user guide/tutorial

https://insidedna.me/tool_page_assets/pdf_manual/fasttree.pdf

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Fastx

Software link to site

http://hannonlab.cshl.edu/fastx_toolkit/

Description

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

Version

0.0.14

Usage instructions

module load fastx/0.0.14

Link to user guide/tutorial

http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

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FEniCS

Software link to site

https://fenicsproject.org/

Description

FEniCS is a popular open-source (LGPLv3) computing platform for solving partial differential equations (PDEs).

Version

2018.2.0.dev0

Usage instructions

module load fenics/2018.2.0.dev0

Link to user guide/tutorial

https://fenicsproject.org/documentation/

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Ffmpeg

Software link to site

https://ffmpeg.org/

Description

FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created.

Version

2.8, 3.4.2

Usage instructions

module load ffmpeg/2.8 or module load ffmpeg/3.4.2

Link to user guide/tutorial

http://ffmpeg.org/documentation.html

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FFTW

Software link to site

http://www.fftw.org/

Description

A collection of fast C routines to compute the discrete Fourier transform.

Version

2.1.5-gcc, 3.3.3-avx, 3.3.3-gcc, 3.3.4-gcc, 3.3.5-intel

Usage instructions

module load fftw/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.fftw.org/#documentation

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fgbio

Software link to site

http://fulcrumgenomics.github.io/fgbio/

Description

A set of tools to analyze genomic data with a focus on Next Generation Sequencing

Version

0.9.0-snapshot

Usage instructions

module load fgbio

Link to user guide/tutorial

http://fulcrumgenomics.github.io/fgbio/

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FImpute

Software link to site

http://animalbiosciences.uoguelph.ca/~msargol/fimpute/

Description

FImpute (ef-impute) was mainly developed for large scale genotype imputation in livestock where hundreds of thousands of individuals are genotypes with different panels.

Version

2.2

Usage instructions

module load fimpute/2.2

Link to user guide/tutorial

http://www.aps.uoguelph.ca/~msargol/fimpute/FImpute_documentation.pdf

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Fix

Software link to site

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX

Description

FMRIB's ICA-based Xnoiseifier for FSL FIX attempts to auto-classify ICA components into good vs bad components.

Version

1.06

Usage instructions

module load fix/1.06

Link to user guide/tutorial

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide

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Flash

Software link to site

https://ccb.jhu.edu/software/FLASH/

Description

FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.

Version

1.2.11

Usage instructions

module load flash/1.2.11

Link to user guide/tutorial

https://ccb.jhu.edu/software/FLASH/

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Flex

Software link to site

https://github.com/westes/flex

Description

None

Version

2.5.39

Usage instructions

module load flex/2.5.39

Link to user guide/tutorial

https://github.com/westes/flex/tree/master/doc

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FLTK

Software link to site

https://www.fltk.org/

Description

A cross-platform C++ GUI toolkit

Version

0.9

Usage instructions

module load clinsv/0.9

Link to user guide/tutorial

https://www.fltk.org/

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Fontconfig

Software link to site

https://www.freedesktop.org/wiki/Software/fontconfig/

Description

None

Version

2.11.92

Usage instructions

module load fontconfig/2.11.92

Link to user guide/tutorial

https://www.freedesktop.org/software/fontconfig/fontconfig-user.html

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fqgrep

Software link to site

https://github.com/indraniel/fqgrep

Description

fqgrep is an approximate sequence pattern matcher for FASTQ/FASTA files.

Version

0.4.4

Usage instructions

module load fqgrep

Link to user guide/tutorial

https://github.com/indraniel/fqgrep

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fqtools

Software link to site

https://github.com/alastair-droop/fqtools

Description

fqtools is a software suite for fast processing of FASTQ files.

Version

2.1

Usage instructions

module load fqtools/2.1

Link to user guide/tutorial

https://github.com/alastair-droop/fqtools

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FragGeneScan

Software link to site

http://omics.informatics.indiana.edu/FragGeneScan/

Description

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes.

Version

1.31

Usage instructions

module load fraggenescan

Link to user guide/tutorial

http://omics.informatics.indiana.edu/FragGeneScan/

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FRANz

Software link to site

https://sourceforge.net/projects/franzpedigree/files/

Description

A pedigree (family tree) reconstruction tool for natural populations.

Version

2.0.0

Usage instructions

module load franz

Link to user guide/tutorial

https://sourceforge.net/projects/franzpedigree/files/

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freebayes

Software link to site

https://github.com/ekg/freebayes

Description

Bayesian haplotype-based polymorphism discovery and genotyping.

Version

1.0.2-33, 1.2.0

Usage instructions

module load freebayes/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/ekg/freebayes

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FreeGLUT

Software link to site

http://freeglut.sourceforge.net/

Description

FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.

Version

2.6.0, 3.0.0

Usage instructions

module load freeglut/xxx (where xxx is the version)

Link to user guide/tutorial

http://freeglut.sourceforge.net/docs/api.php

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Freesurfer

Software link to site

https://surfer.nmr.mgh.harvard.edu/

Description

A set of automated tools for reconstruction of the brains cortical surface from structural MRI data.

Version

dev, 5.3.0, 6.0, 6.0.0, 6.0.1

Usage instructions

module load freesurfer/xxx (where xxx is the version)

Link to user guide/tutorial

https://surfer.nmr.mgh.harvard.edu/fswiki

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Freetype

Software link to site

https://www.freetype.org/

Description

None

Version

2.5.5

Usage instructions

module load freetype/2.5.5

Link to user guide/tutorial

https://www.freetype.org/freetype2/docs/documentation.html

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Freexl

Software link to site

https://www.gaia-gis.it/fossil/freexl/index

Description

FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.

Version

1.0.2

Usage instructions

module load freexl/1.0.2

Link to user guide/tutorial

http://www.gaia-gis.it/gaia-sins/freexl-1.0.1-doxy-doc/html/index.html

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Fsl

Software link to site

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL

Description

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Version

5.0.8, 5.0.9, 6.0.1

Usage instructions

module load fsl/xxx (where xxx is the version)

Link to user guide/tutorial

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support

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funannotate

Software link to site

https://github.com/nextgenusfs/funannotate

Description

Funannotate is a pipeline for genome annotation (built specifically for fungi, but theoretically should work with other eukaryotes).

Version

0.7.2, 1.2

Usage instructions

module load funannotate/0.72 or module load funannotate/1.2

Link to user guide/tutorial

https://github.com/nextgenusfs/funannotate/wiki

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FUSTr

Software link to site

https://github.com/tijeco/FUSTr

Description

Fuster is a pipeline that clusters coding sequences from transcriptomes into protein families, and then analyzes those families for positive selection.

Version

0.0.0

Usage instructions

module load fustr

Link to user guide/tutorial

https://github.com/tijeco/FUSTr

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GadgetViewer

Software link to site

http://astro.dur.ac.uk/~jch/gadgetviewer/index.html

Description

This is a program for interactive visualisation of Gadget N-body simulation snapshots.

Version

1.0.7

Usage instructions

module load gadgetviewer/1.0.7

Link to user guide/tutorial

http://astro.dur.ac.uk/~jch/gadgetviewer/index.html#docs

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Gamos

Software link to site

http://fismed.ciemat.es/GAMOS/

Description

GAMOS is a GEANT4-based framework that is at the same time easy-to-use and flexible.

Version

5.0.0

Usage instructions

module load gamos/5.0.0

Link to user guide/tutorial

http://fismed.ciemat.es/GAMOS/gamos_userguide.php

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gatb

Software link to site

https://github.com/GATB/gatb-core

Description

The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets.

Version

1.1.0 and1.2.1

Usage instructions

module load gatb

Link to user guide/tutorial

https://github.com/GATB/gatb-core

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Gate

Software link to site

http://www.opengatecollaboration.org/

Description

GATE is an advanced open source software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy.

Version

6.2, 7.1, 7.2

Usage instructions

module load gate/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.opengatecollaboration.org/UsersGuide

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Gatk

Software link to site

https://software.broadinstitute.org/gatk/

Description

The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data.

Version

3.3.0, 3.4.0, 3.6.0, 3.7.0, 3.8.0, 3.8.1, 4.0.2.1, 4.0.8.1

Usage instructions

module load gatk/xxx (where xxx represents version number)

Link to user guide/tutorial

https://software.broadinstitute.org/gatk/documentation/quickstart

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gaussian

Software link to site

http://gaussian.com/

Description

Gaussian predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments.

Version

g16

Usage instructions

https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/229245086/Gaussian

Link to user guide/tutorial

http://gaussian.com/man/

Special licensing notes

By using Gaussian you are agreeing to be bound by the following terms and conditions.

If Gaussian is used to obtain a result, and that result is published in the public literature, then you agree to acknowledge its use in an appropriate citation.
The citation should include:

a. the name of the product (Gaussian 16);
b. the source (Gaussian, Inc., 340 Quinnipiac Street, Building 40, Wallingford, CT 06492);
c. the authorship as designated by GAUSSIAN; and
d. an appropriate copyright notice as designated by GAUSSIAN.

Alternatively, the citation may be made in the form of a reference to a published scientific journal article as designated by GAUSSIAN.

Visit

http://gaussian.com/citation/

for detailed citation requirements.

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gawk

Software link to site

https://www.gnu.org/software/gawk/

Description

GNU AWK later version

Version

5.0.0

Usage instructions

module load gawk

Link to user guide/tutorial

https://www.gnu.org/software/gawk/manual/gawk.html

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Gblocks

Software link to site

http://molevol.cmima.csic.es/castresana/Gblocks.html

Description

Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.

Version

0.91b

Usage instructions

module load gblocks/0.91b

Link to user guide/tutorial

http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html

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gcc

Software link to site

https://gcc.gnu.org/

Description

GNU Compiler Collection

Version

4.8.4, 4.9.0, 4.9.3, 4.9.4, 4.9.4.1, 5.4.0, 6.1.0, 6.2.0, 7.2.0, 9.1.0

Usage instructions

module load gcc/xxx (where xxxx represents version number)

Link to user guide/tutorial

https://gcc.gnu.org/onlinedocs/

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gcta

Software link to site

http://cnsgenomics.com/software/gcta/download.html

Description

GCTA (Genome-wide Complex Trait Analysis)

Version

1.26.0, 1.92.0

Usage instructions

module load gcta/xxx (where xxx is the version)

Link to user guide/tutorial

http://cnsgenomics.com/software/gcta/download.html

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Gdal

Software link to site

http://www.gdal.org/

Description

GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats.

Version

1.11.2, 2.3.1

Usage instructions

module load gdal/xx (where xxx is the version number)

Link to user guide/tutorial

https://trac.osgeo.org/gdal/

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Gdb

Software link to site

https://www.sourceware.org/gdb/

Description

The GNU Debugger (GDB) is the standard debugger for the GNU software system.

Version

7.6.1

Usage instructions

module load gdb/7.6.1

Link to user guide/tutorial

https://sourceware.org/gdb/download/onlinedocs/

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GDC-Client

Software link to site

https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

Description

The GDC Data Transfer Tool provides an optimised method of transferring data to and from the GDC, and enables resumption of interrupted transfers.

Version

1.2.0, 1.4.0

Usage instructions

module load gdc-client/xxx (where xxx is the version)

Link to user guide/tutorial

https://docs.gdc.cancer.gov/Data_Transfer_Tool/PDF/Data_Transfer_Tool_UG.pdf

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Gdl

Software link to site

http://gnudatalanguage.sourceforge.net/

Description

GNU Data Language (GDL).

Version

0.9.6

Usage instructions

module load gdl/0.9.6

Link to user guide/tutorial

http://gnudatalanguage.sourceforge.net/documentation.php

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Geant4

Software link to site

http://geant4.web.cern.ch/geant4/

Description

Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

Version

4.9.5, 4.10.01,4.10.02

Usage instructions

module load geant4/xxx (where xxx represents version number)

Link to user guide/tutorial

http://geant4.web.cern.ch/geant4/support/gettingstarted.shtml

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gem-tools

Software link to site

https://github.com/gemtools/gemtools

Description

GEM-Tools is a C API to support and simplify usage of the GEM Mapper.

Version

1.7.1-i3

Usage instructions

module load gemtools

Link to user guide/tutorial

https://github.com/gemtools/gemtools/blob/master/Readme.md

Special licensing notes

GPL

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Gemma

Software link to site

http://www.xzlab.org/software.html

Description

Genome-wide Efficient Mixed Model Association

Version

0.93

Usage instructions

module load gemma/0.93

Link to user guide/tutorial

http://www.xzlab.org/software/GEMMAmanual.pdf

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GeneMark-ES

Software link to site

http://exon.gatech.edu/GeneMark/

Description

Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes.

Version

4.21, 4.33

Usage instructions

module load genemark-es/4.21 or module load genemark-es/4.33

Link to user guide/tutorial

http://exon.gatech.edu/GeneMark/background.html

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gengetopt

Software link to site

https://www.systutorials.com/docs/linux/man/1-gengetopt/

Description

Gengetopt is a tool to generate C code to parse the command line arguments argc and argv that are part of every C or C++ program.

Version

2.22

Usage instructions

module load gengetopt

Link to user guide/tutorial

https://www.systutorials.com/docs/linux/man/1-gengetopt/

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Genomemasker

Software link to site

http://bioinfo.ut.ee/?page_id=167

Description

GenomeMasker (gmasker) masks over-represented words in the FASTA file, preventing design of primers in repeated regions.

Version

1.3

Usage instructions

module load genomemasker

Link to user guide/tutorial

http://bioinfo.ut.ee/download/dl.php?file=12

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GenomeTools

Software link to site

http://genometools.org/

Description

A free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary.

Version

1.5.9

Usage instructions

module load genometools/1.5.9

Link to user guide/tutorial

http://genometools.org/documentation.html

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Geos

Software link to site

https://trac.osgeo.org/geos/

Description

GEOS (Geometry Engine- Open Source) is a C++ port of the Java Topology Suite (JTS). The JTS Topology Suite is an API of spatial predicates and functions for processing geometry.

Version

3.5.0

Usage instructions

module load geos/3.5.0

Link to user guide/tutorial

https://trac.osgeo.org/geos/wiki/TracGuide

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Gephi

Software link to site

https://gephi.org/

Description

Visualization and exploration software for all kinds of graphs and networks.

Version

0.9.2

Usage instructions

module load gephi

Link to user guide/tutorial

https://gephi.org/users/

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Gess

Software link to site

http://www.gess-inc.com/gess/support-software.html?sl=EN

Description

A graph-based exon-skipping scanner detection program for RNA-seq data.

Version

1

Usage instructions

None

Link to user guide/tutorial

http://www.gess-inc.com/gess/support-faq.html

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Gettext

Software link to site

https://www.gnu.org/software/gettext/

Description

GNU gettext package

Version

0.19.8

Usage instructions

module load gettext/0.19.8

Link to user guide/tutorial

https://www.gnu.org/software/gettext/manual/index.html

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Gflags

Software link to site

https://github.com/gflags/gflags

Description

A C++ library that implements command line flags processing.

Version

2.1.2, 2.2.1

Usage instructions

module load gflags/2.1.2 or module load gflags/2.2.1

Link to user guide/tutorial

https://gflags.github.io/gflags/

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GHMM

Software link to site

http://ghmm.sourceforge.net/index.html

Description

The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions. It comes with Python wrappers which provide a much nicer interface and added functionality. The GHMM is licensed under the LGPL.

Version

0.9-rc3

Usage instructions

module load ghmm

Link to user guide/tutorial

http://ghmm.sourceforge.net/documentation.html

Special licensing notes

LGPL

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Ghostscript

Software link to site

https://www.ghostscript.com/

Description

None

Version

9.15

Usage instructions

module load ghostscript/9.15

Link to user guide/tutorial

https://ghostscript.com/doc/9.15/Readme.htm

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giremi

Software link to site

https://github.com/zhqingit/giremi

Description

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data

Version

0.3.1

Usage instructions

module load giremi

Link to user guide/tutorial

https://github.com/zhqingit/giremi

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Git

Software link to site

https://git-scm.com/

Description

A version control system for software development and other version control tasks.

Version

2.14.1, 2.16.2

Usage instructions

module load git/2.14.1 or module load git/2.16.2

Link to user guide/tutorial

https://git-scm.com/doc

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GL2PS

Software link to site

http://www.geuz.org/gl2ps/

Description

An OpenGL to PostScript printing library

Version

1.4.0

Usage instructions

module load gl2ps/1.4.0

Link to user guide/tutorial

http://www.geuz.org/gl2ps/

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Glib

Software link to site

https://developer.gnome.org/glib/

Description

None

Version

2.34.0

Usage instructions

module load glib/2.34.0

Link to user guide/tutorial

https://developer.gnome.org/glib/2.34/

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Glog

Software link to site

https://github.com/google/glog

Description

C++ implementation of the Google logging module.

Version

0.3.3

Usage instructions

module load glog/0.3.3

Link to user guide/tutorial

http://htmlpreview.github.io/?https://github.com/google/glog/blob/master/doc/glog.html

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gmap

Software link to site

http://research-pub.gene.com/gmap/

Description

GMAP - A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP - Genomic Short-read Nucleotide Alignment Program

Version

2017-06-20 00:00:00

Usage instructions

module load gmap

Link to user guide/tutorial

http://research-pub.gene.com/gmap/

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GMP

Software link to site

https://gmplib.org/

Description

GNU Multiple Precision Arithmetic Library.

Version

4.3.2, 5.1.3, 6.1.0, 6.1.2

Usage instructions

module load gmp/xxx (where xxx represents version number)

Link to user guide/tutorial

https://gmplib.org/manual/

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Gmsh

Software link to site

http://gmsh.info/

Description

A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities

Version

4.1.5, 4.2

Usage instructions

module load gmsh/xxx (where xxx is the version)

Link to user guide/tutorial

http://gmsh.info/doc/texinfo/gmsh.html

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Gnuplot

Software link to site

http://www.gnuplot.info/

Description

Gnuplot is a portable command-line driven graphing utility.

Version

4.6.6, 5.0.0, 5.0.5

Usage instructions

module load gnuplot/5.0.0 or module load gnuplot/5.0.5

Link to user guide/tutorial

http://www.gnuplot.info/docs_5.0/gnuplot.pdf

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Go

Software link to site

https://golang.org/

Description

Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.

Version

1.8.3, 1.12.7

Usage instructions

module load golang/xxx (where xxx is the version)

Link to user guide/tutorial

https://golang.org/doc/

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Gperftools

Software link to site

https://github.com/gperftools/gperftools

Description

gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools.

Version

2.5

Usage instructions

module load gperftools/2.5

Link to user guide/tutorial

https://github.com/gperftools/gperftools/wiki

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GPS-Lipid

Software link to site

http://lipid.biocuckoo.org/

Description

A robust tool for the prediction of multiple lipid modification sites

Version

1

Usage instructions

module load gps-lipid

Link to user guide/tutorial

http://lipid.biocuckoo.org/userguide.php

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Graphicsmagick

Software link to site

http://www.graphicsmagick.org/

Description

A set of command line tools and programming APIs for manipulating, editing, and converting raster and vector images.

Version

1.3.23

Usage instructions

module load graphicsmagick/1.3.23

Link to user guide/tutorial

http://www.graphicsmagick.org/reference.html

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GraPhlAn

Software link to site

https://huttenhower.sph.harvard.edu/graphlan

Description

GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.

Version

0.9.7

Usage instructions

module load graphlan/0.9.7

Link to user guide/tutorial

https://bitbucket.org/biobakery/biobakery/wiki/Home

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GraPhlAn

Software link to site

https://huttenhower.sph.harvard.edu/graphlan

Description

GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.

Version

0.9.7

Usage instructions

module load graphlan/0.9.7

Link to user guide/tutorial

https://bitbucket.org/biobakery/biobakery/wiki/Home

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Graphviz

Software link to site

http://www.graphviz.org/

Description

None

Version

2.38.0

Usage instructions

module load graphviz/2.38.0

Link to user guide/tutorial

http://www.graphviz.org/Documentation.php

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GRIDSS

Software link to site

https://github.com/PapenfussLab/gridss

Description

The Genomic Rearrangement IDentification Software Suite

Version

1.7.0, 2.0.1

Usage instructions

module load gridss/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/PapenfussLab/gridss

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Gromacs

Software link to site

http://www.gromacs.org/

Description

Molecular dynamics simulation package.

Version

4.6.7, 5.1, 5.1.4, 2016.2, 2018.2, 2019.1

Usage instructions

Type "module avail gromacs" on an Artemis login node to see available versions

Link to user guide/tutorial

http://manual.gromacs.org/documentation/

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Gromacs-Plumed

Software link to site

http://www.plumed.org/

Description

Molecular dynamics simulation package.

Version

5.1.4-openmpi-gcc-plumed-2.2.4, 5.1.4-openmpi-gcc-plumed-2.3.0

Usage instructions

module load gromacs-plumed/5.1.4-openmpi-gcc-plumed-2.2.4 or module load gromacs-plumed/5.1.4-openmpi-gcc-plumed-2.3.0

Link to user guide/tutorial

http://plumed.github.io/doc-v2.0/user-doc/html/index.html

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Gsl

Software link to site

https://www.gnu.org/software/gsl/

Description

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.

Version

1.16, 2.3

Usage instructions

module load gsl/1.16 or module load gsl/2.3

Link to user guide/tutorial

https://www.gnu.org/software/gsl/manual/html_node/

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gtextutils

Software link to site

https://github.com/agordon/libgtextutils

Description

Gordon-Text_utils-Library

Version

0.6

Usage instructions

module load gtextutils

Link to user guide/tutorial

https://github.com/agordon/libgtextutils

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GTFTools

Software link to site

http://www.genemine.org/gtftools.php

Description

GTFtools provides a set of functions to analyze various modes of gene models

Version

0.6.5

Usage instructions

module load gtftools

Link to user guide/tutorial

http://www.genemine.org/gtftools.php

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GTS

Software link to site

http://gts.sourceforge.net/

Description

The GNU Triangulated Surface Library

Version

121130

Usage instructions

module load gts/121130

Link to user guide/tutorial

http://gts.sourceforge.net/reference/book1.html

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Gubbins

Software link to site

http://sanger-pathogens.github.io/gubbins/

Description

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.

Version

1.4.1, 2.3.4

Usage instructions

module load gubbins/xxx (where xxx is the version)

Link to user guide/tutorial

ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/GubbinsManual_latest.pdf

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Guile

Software link to site

https://www.gnu.org/software/guile/

Description

LIBGUILE Project GNU extension language library.

Version

1.8.2, 2.0.13

Usage instructions

module load guile/1.8.2 or module load guile/2.0.13

Link to user guide/tutorial

https://www.gnu.org/software/guile/learn/

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Gurobi

Software link to site

http://www.gurobi.com/

Description

GUROBI optimization solver

Version

7.5.1, 8.0.1

Usage instructions

module load gurobi/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.gurobi.com/documentation/

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Haddock

Software link to site

http://www.bonvinlab.org/software/haddock2.2/

Description

Haddock is a versatile information-driven flexible docking approach for the modelling of biomolecular complexes.

Version

2

Usage instructions

module load haddock/2

Link to user guide/tutorial

http://www.bonvinlab.org/software/haddock2.2/manual/

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hapcut

Software link to site

https://github.com/vibansal/hapcut

Description

HapCUT is a max-cut based algorithm for haplotype assembly

Version

0.7, 2, 2-1.1

Usage instructions

module load hapcut/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/vibansal/hapcut

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Hapcut

Software link to site

https://github.com/vibansal/hapcut

Description

HapCUT is a max-cut based algorithm for haplotype assembly that uses the mix of sequenced fragments from the two chromosomes of an individual, this program can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM

Version

0.7

Usage instructions

module load hapcut/0.7

Link to user guide/tutorial

https://github.com/vibansal/hapcut

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Hapflow

Software link to site

http://mjsull.github.io/HapFlow/

Description

HapFlow is a python application for visualising haplotypes present in sequencing data.

Version

1.1.2

Usage instructions

module load hapflow/1.1.2

Link to user guide/tutorial

https://github.com/mjsull/HapFlow/wiki

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haplotyper

Software link to site

http://www.people.fas.harvard.edu/~junliu/Haplo/click.html

Description

HAPLOTYPER is a software for haplotype inference using the Bayesian algorithm

Version

1

Usage instructions

module load haplotyper

Link to user guide/tutorial

http://www.people.fas.harvard.edu/~junliu/Haplo/docMain.htm

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Haploview

Software link to site

https://www.broadinstitute.org/haploview/haploview

Description

Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.

Version

4.2

Usage instructions

module load haploview/4.2

Link to user guide/tutorial

https://www.broadinstitute.org/haploview/user-manual

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Hapsembler

Software link to site

http://compbio.cs.toronto.edu/hapsembler/index.html

Description

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism.

Version

2.21

Usage instructions

module load hapsembler/2.21

Link to user guide/tutorial

http://compbio.cs.toronto.edu/hapsembler/hapsembler-2.21_manual.pdf

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Harfbuzz

Software link to site

https://www.freedesktop.org/wiki/Software/HarfBuzz/

Description

None

Version

0.9.38

Usage instructions

module load harfbuzz/0.9.38

Link to user guide/tutorial

https://github.com/behdad/harfbuzz/wiki

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HDF5

Software link to site

https://support.hdfgroup.org/HDF5/

Description

HDF5 is a data model, library, and file format for storing and managing data. Type "module avail hdf5" on the Artemis command line for a full list of installed HDF5 versions

Version

1.8.14, 1.8.16

Usage instructions

module load hdf5/1.8.14 or module load hdf5/1.8.16

Link to user guide/tutorial

https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-Responsive%20HTML5/index.html

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HEALPix

Software link to site

https://healpix.sourceforge.io/

Description

Software for pixelisation, hierarchical indexation, synthesis, analysis, and visualisation of data on the sphere.

Version

2.15a, 2.20a

Usage instructions

module load healpix/xxx (where xxx is the version)

Link to user guide/tutorial

https://healpix.sourceforge.io/documentation.php

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Hh-Suite

Software link to site

https://github.com/soedinglab/hh-suite

Description

Remote protein homology detection suite.

Version

3.0.0

Usage instructions

module load hh-suite/3.0.0

Link to user guide/tutorial

https://github.com/soedinglab/hh-suite

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HiC-bench

Software link to site

https://github.com/NYU-BFX/hic-bench

Description

A set of pipelines for Hi-C and ChIP-Seq analysis.

Version

3.0.0

Usage instructions

module load hic-bench

Link to user guide/tutorial

https://github.com/NYU-BFX/hic-bench_documentation/blob/master/HiC-Bench_manual.pdf

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HiCUP

Software link to site

https://www.bioinformatics.babraham.ac.uk/projects/hicup/

Description

A bioinformatics pipeline for processing Hi-C data.

Version

0.6.1

Usage instructions

module load hicup

Link to user guide/tutorial

https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html

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Highwayhash

Software link to site

https://github.com/google/highwayhash

Description

Fast and strong hash functions.

Version

0.0.0

Usage instructions

module load highwayhash/0.0.0

Link to user guide/tutorial

https://github.com/google/highwayhash

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Hiredis

Software link to site

https://github.com/redis/hiredis

Description

Hiredis is a minimalistic C client library for the Redis database.

Version

0.13.3, 5.2.2

Usage instructions

module load hiredis/0.13.3 or module load hiredis/5.2.2

Link to user guide/tutorial

https://github.com/redis/hiredis

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HISAT2

Software link to site

https://ccb.jhu.edu/software/hisat2/index.shtml

Description

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome)

Version

2.1.0

Usage instructions

module load hisat2/2.1.0

Link to user guide/tutorial

https://ccb.jhu.edu/software/hisat2/manual.shtml

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hlascan

Software link to site

http://www.genomekorea.com/display/tools/HLAscan

Description

HLAscan is an alignment-based program that determines haplotypes taking read distribution into account.

Version

4

Usage instructions

module load hlascan

Link to user guide/tutorial

http://www.genomekorea.com/display/tools/HLAscan

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hmftools

Software link to site

https://github.com/hartwigmedical/hmftools

Description

Various utility tools for working with genomics data

Version

4.5

Usage instructions

module load hmftools

Link to user guide/tutorial

https://github.com/hartwigmedical/hmftools

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Hmmer

Software link to site

http://hmmer.org/

Description

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments.

Version

3.1b2, 3.2

Usage instructions

module load hmmer/xxx (where xxx is the version number)

Link to user guide/tutorial

http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf

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Homer

Software link to site

http://homer.ucsd.edu/homer/

Description

Software for motif discovery and next generation sequencing analysis.

Version

4.9.1

Usage instructions

module load homer/4.9.1

Link to user guide/tutorial

http://homer.ucsd.edu/homer/

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Hoomd

Software link to site

https://glotzerlab.engin.umich.edu/hoomd-blue/

Description

A general-purpose particle simulation toolkit.

Version

1.3.3, 1.3.3-python3

Usage instructions

module load hoomd/1.3.3 or module load hoomd/1.3.3-python3

Link to user guide/tutorial

http://hoomd-blue.readthedocs.io/en/stable/

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hotspotter

Software link to site

http://stephenslab.uchicago.edu/software.html#hotspotter

Description

Software for identifying recombination hotspots from population SNP data.

Version

1.2.1-modified

Usage instructions

module load hotspotter

Link to user guide/tutorial

http://stephenslab.uchicago.edu/assets/papers/Li2003.pdf

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HPC GridRunner

Software link to site

https://github.com/HpcGridRunner/HpcGridRunner

Description

HPC GridRunner is a simple command-line interface to high throughput computing using a variety of different grid computing platforms

Version

1.0.2

Usage instructions

module load hpcgridrunner

Link to user guide/tutorial

https://github.com/HpcGridRunner/HpcGridRunner.github.io/wiki

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HTSlib

Software link to site

http://www.htslib.org/

Description

A C library for high-throughput sequencing data formats

Version

1.2.1, 1.3.1, 1.5, 1.5-intel, 1.6, 1.6-intel, 1.9

Usage instructions

module load htslib/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.htslib.org/doc/

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HYPRE

Software link to site

https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods

Description

HYPRE: Scalable Linear Solvers and Multigrid Methods

Version

2.11.2

Usage instructions

module load hypre/2.11.2

Link to user guide/tutorial

https://computation.llnl.gov/sites/default/files/public/hypre-2.11.2_usr_manual.pdf

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I-Tasser

Software link to site

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Description

An integrated package for protein structure and function predictions.

Version

4.3, 4.4

Usage instructions

module load i-tasser/4.3 or module load i-tasser/4.4

Link to user guide/tutorial

http://zhanglab.ccmb.med.umich.edu/I-TASSER/FAQ.html

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Icmake

Software link to site

https://fbb-git.github.io/icmake/

Description

A program maintenance utility.

Version

7.22.01

Usage instructions

module load icmake/7.22.01

Link to user guide/tutorial

https://fbb-git.github.io/icmake/

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Icu

Software link to site

http://site.icu-project.org/

Description

None

Version

54.1

Usage instructions

module load icu/54.1

Link to user guide/tutorial

http://userguide.icu-project.org/

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Idba

Software link to site

http://i.cs.hku.hk/~alse/hkubrg/projects/idba/

Description

None

Version

1.1.2

Usage instructions

module load idba/1.1.2

Link to user guide/tutorial

http://hoomd-blue.readthedocs.io/en/stable/

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Idl

Software link to site

http://www.harrisgeospatial.com/ProductsandSolutions/GeospatialProducts/IDL.aspx

Description

IDL is a scientific programming language used to extract visualizations from complex numerical data.

Version

80

Usage instructions

module load idl/80

Link to user guide/tutorial

http://www.harrisgeospatial.com/ProductsandSolutions/GeospatialProducts/IDL.aspx

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idp

Software link to site

https://github.com/bioinform/IDP

Description

IDP is a statistical isoform prediction method to construct possible isoform candidates from the union of long reads and short reads with spliced alignment

Version

0.1.7

Usage instructions

module load idp

Link to user guide/tutorial

https://github.com/bioinform/IDP

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Igvtools

Software link to site

http://data.broadinstitute.org/igv/projects/downloads/igvtools_2.3.91.zip

Description

The Integrative Genomics Viewer (IGV)

Version

2.3.91

Usage instructions

module load igvtools

Link to user guide/tutorial

http://www.broadinstitute.org/software/igv/igvtools_commandline

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IL

Software link to site

http://openil.sourceforge.net/

Description

Cross platform image library

Version

1.8.0

Usage instructions

module load il

Link to user guide/tutorial

http://openil.sourceforge.net/docs/

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Imagej

Software link to site

https://imagej.nih.gov/ij/

Description

Image Processing and Analysis in Java.

Version

148

Usage instructions

module load imagej/148

Link to user guide/tutorial

https://imagej.nih.gov/ij/docs/index.html

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Imagemagick

Software link to site

https://www.imagemagick.org/script/index.php

Description

A software suite to create, edit, compose, or convert bitmap images.

Version

6.9.2-3

Usage instructions

module load imagemagick/6.9.2-3

Link to user guide/tutorial

https://www.imagemagick.org/discourse-server/viewtopic.php?f=1&t=9620

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Imp

Software link to site

https://integrativemodeling.org/

Description

IMP is an open source C++ and Python toolbox for solving complex biomolecular modeling problems

Version

2.4.0, 2.5.0, 2.6.0

Usage instructions

module load imp/xxx (where xxx represents version number)

Link to user guide/tutorial

https://integrativemodeling.org/doc.html

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IMPUTE2

Software link to site

http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Description

IMPUTE2 is a genotype imputation and haplotype phasing program

Version

2.3.2

Usage instructions

module load impute2/2.3.2

Link to user guide/tutorial

http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

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Infernal

Software link to site

http://eddylab.org/infernal/

Description

Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.

Version

1.1.1

Usage instructions

module load infernal/1.1.1

Link to user guide/tutorial

http://eddylab.org/infernal/Userguide.pdf

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Intel

Software link to site

https://software.intel.com/en-us/intel-compilers

Description

Intel Compiler Suite.

Version

15.1, 18.1

Usage instructions

module load intel/15.1 or module load intel/18.1

Link to user guide/tutorial

https://software.intel.com/en-us/intel-compilers

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Intel-MPI

Software link to site

https://software.intel.com/en-us/intel-mpi-library

Description

Intel MPI libraries.

Version

15.1, 18.1

Usage instructions

module load intel-mpi/15.1 or module load intel-mpi/18.1

Link to user guide/tutorial

https://software.intel.com/en-us/intel-mpi-library/documentation

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InterProScan

Software link to site

https://www.ebi.ac.uk/interpro/

Description

Protein sequence analysis and classification

Version

5.28-67.0, 5.34-73.0, 5.36-75.0

Usage instructions

module load interproscan/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.ebi.ac.uk/interpro/training.html

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Intltool

Software link to site

https://freedesktop.org/wiki/Software/intltool/

Description

Utility scripts for internationalizing XML.

Version

0.51.0

Usage instructions

module load intltool/0.51.0

Link to user guide/tutorial

https://freedesktop.org/wiki/Software/intltool/

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IQ-TREE

Software link to site

http://www.iqtree.org/

Description

Efficient software for phylogenomic inference

Version

1.6.7

Usage instructions

module load iqtree

Link to user guide/tutorial

http://www.iqtree.org/doc/

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Is_Mapper

Software link to site

https://github.com/jhawkey/IS_mapper

Description

This program takes paired end Illumina short read sequence data, an IS query of interest and a reference genome or assembly and reports the locations of the IS query in the reference genome or the assembly.

Version

0.1.3

Usage instructions

module load is_mapper/0.1.3

Link to user guide/tutorial

https://github.com/jhawkey/IS_mapper

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ITSx

Software link to site

http://microbiology.se/software/itsx/

Description

ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.

Version

1.0.11, 1.1b

Usage instructions

module load itsx/xxx (where xxx is the version number)

Link to user guide/tutorial

http://microbiology.se/software/itsx/

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Iva

Software link to site

http://sanger-pathogens.github.io/iva/

Description

IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.

Version

1.0.3

Usage instructions

module load iva/1.0.3

Link to user guide/tutorial

http://sanger-pathogens.github.io/iva/

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Jags

Software link to site

http://mcmc-jags.sourceforge.net/

Description

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Version

3.4.0, 4.2.0

Usage instructions

module load jags/3.4.0 or module load jags/4.2.0

Link to user guide/tutorial

https://sourceforge.net/projects/mcmc-jags/files/Manuals/3.x/jags_user_manual.pdf/download

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Jaspa

Software link to site

https://github.com/mdcao/japsa

Description

Jaspa is a free, open source Java package for sequence analysis.

Version

1.7-10a

Usage instructions

module load jaspa/1.7-10a

Link to user guide/tutorial

http://japsa.readthedocs.io/en/latest/

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Jasper

Software link to site

https://www.ece.uvic.ca/~frodo/jasper/

Description

An open-source initiative to provide a free software-based reference implementation of the JPEG-2000 codec.

Version

1.900.1

Usage instructions

module load jasper/1.900.1

Link to user guide/tutorial

https://www.ece.uvic.ca/~frodo/jasper/#doc

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Java

Software link to site

http://www.oracle.com/technetwork/java/index.html

Description

Java development programs and run-time libraries.

Version

jdk1.7.0_80, jdk1.8.0_111, jdk1.8.0_31, jdk1.8.0_45, jdk1.8.0_212, jdk-12.0.1

Usage instructions

module load java/xxx (where xxx represents version number)

Link to user guide/tutorial

https://java.com/en/download/help/

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Jellyfish

Software link to site

http://www.cbcb.umd.edu/software/jellyfish/

Description

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.

Version

1.1.10, 2.2.6

Usage instructions

module load jellyfish/1.1.10 or module load jellyfish/2.2.26

Link to user guide/tutorial

http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf

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jq

Software link to site

https://stedolan.github.io/jq/

Description

jq is a lightweight and flexible command-line JSON processor.

Version

1.5

Usage instructions

module load jq/1.5

Link to user guide/tutorial

https://stedolan.github.io/jq/manual/

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Juicer

Software link to site

https://omictools.com/juicer-tool

Description

Juicer pipeline automatically builds the Hi-C maps and annotates features.

Version

1.5

Usage instructions

module load juicer/1.5

Link to user guide/tutorial

https://github.com/theaidenlab/juicer/blob/master/README.md

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Julia

Software link to site

http://julialang.org/

Description

Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.

Version

0.5.0, 0.6.0

Usage instructions

module load julia/0.5.0 or module load julia/0.6.0

Link to user guide/tutorial

http://docs.julialang.org/en/stable/#manual

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Jupyter

Software link to site

http://jupyter.org/

Description

The Jupyter Notebook is a web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text.

Version

base

Usage instructions

module load jupyter/base

Link to user guide/tutorial

https://jupyter.readthedocs.io/en/latest/index.html

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Kalign

Software link to site

http://msa.sbc.su.se/cgi-bin/msa.cgi

Description

A fast and accurate multiple sequence alignment algorithm.

Version

2.04

Usage instructions

module load kalign

Link to user guide/tutorial

http://msa.sbc.su.se/cgi-bin/msa.cgi

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kallisto

Software link to site

https://pachterlab.github.io/kallisto/download

Description

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data

Version

0.43.1

Usage instructions

module load kallisto

Link to user guide/tutorial

https://pachterlab.github.io/kallisto/download

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Kat

Software link to site

https://github.com/TGAC/KAT

Description

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

Version

2.0.6

Usage instructions

module load kat/2.0.6

Link to user guide/tutorial

https://github.com/TGAC/KAT

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kentutils

Software link to site

https://github.com/bowhan/kent/tree/master/src/userApps

Description

UCSC genome browser 'kent' bioinformatic utilities

Version

348, 360

Usage instructions

module load kentutils/348 or module load kentutils/360

Link to user guide/tutorial

https://github.com/bowhan/kent/tree/master/src/userApps

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KMA

Software link to site

https://bitbucket.org/genomicepidemiology/kma/src/master/

Description

KMA is a mapping method designed to map raw reads directly against redundant databases

Version

1.1.4, 1.2.10a, 1.2.4

Usage instructions

module load kma/xxx (where xxx is the version)

Link to user guide/tutorial

https://bitbucket.org/genomicepidemiology/kma/src/master/

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Kmc

Software link to site

http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about

Description

KMC K-mer Counter is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.

Version

2.1.1

Usage instructions

module load kmc/2.1.1

Link to user guide/tutorial

http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=download

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KohGPI

Software link to site

http://gpi.unibe.ch/

Description

Identification of GPI-anchor signals by a Kohonen Self Organizing Map

Version

1.5

Usage instructions

module load kohgpi

Link to user guide/tutorial

http://gpi.unibe.ch/

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Kraken

Software link to site

https://ccb.jhu.edu/software/kraken/

Description

Kraken is a system for assigning taxonomic labels to short DNA sequences.

Version

0.10.5-beta, 1.0

Usage instructions

module load kraken/0.10.5-beta or module load kraken/1.0

Link to user guide/tutorial

https://ccb.jhu.edu/software/kraken/

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Kraken2

Software link to site

https://ccb.jhu.edu/software/kraken/

Description

The second version of the Kraken taxonomic sequence classification system. Kraken is a system for assigning taxonomic labels to short DNA sequences

Version

1, 2.0.6-beta, 2.0.7-beta

Usage instructions

module load kraken2/xxx (where xxx is the version number)

Link to user guide/tutorial

https://ccb.jhu.edu/software/kraken/

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KronaTools

Software link to site

https://github.com/marbl/Krona

Description

Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.

Version

2.7, 2.7.1

Usage instructions

module load kronatools

Link to user guide/tutorial

https://github.com/marbl/Krona/wiki/KronaTools

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kSNP

Software link to site

https://sourceforge.net/projects/ksnp/

Description

kSNP does SNP discovery and SNP annotation from whole genomes

Version

3.1

Usage instructions

module load ksnp/3.1

Link to user guide/tutorial

https://sourceforge.net/projects/ksnp/

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Lammps

Software link to site

http://lammps.sandia.gov/

Description

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

Version

20150210, 20163007-test, 20163007, 20161711, 20172601, 20181603

Usage instructions

module load lammps/xxx (where xxx represents version number)

Link to user guide/tutorial

http://lammps.sandia.gov/doc/Manual.html

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Lapack

Software link to site

http://www.netlib.org/lapack/

Description

Library for high performance linear algebra computations.

Version

3.5.0, 3.8.0

Usage instructions

module load lapack/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.netlib.org/lapack/#_documentation

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LAST

Software link to site

http://last.cbrc.jp/

Description

LAST finds similar regions between sequences.

Version

894

Usage instructions

module load last/894

Link to user guide/tutorial

http://last.cbrc.jp/doc/last-tutorial.html

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LASTZ

Software link to site

http://www.bx.psu.edu/~rsharris/lastz/

Description

LASTZ is a program for aligning DNA sequences, a pairwise aligner.

Version

1.03.73, 1.04

Usage instructions

module load lastz/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.bx.psu.edu/~rsharris/lastz/

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Leveldb

Software link to site

https://github.com/google/leveldb

Description

LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values.

Version

1.14, 1.16

Usage instructions

module load leveldb/1.14 or module load leveldb/1.16

Link to user guide/tutorial

https://github.com/google/leveldb

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Libcroco

Software link to site

https://github.com/GNOME/libcroco

Description

None

Version

0.6.8

Usage instructions

module load libcroco/0.6.8

Link to user guide/tutorial

https://github.com/GNOME/libcroco/tree/master/docs

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Libcurl

Software link to site

https://curl.haxx.se/libcurl/

Description

None

Version

7.40.0

Usage instructions

module load libcurl/7.40.0

Link to user guide/tutorial

https://curl.haxx.se/libcurl/c/libcurl-tutorial.html

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Libelf

Software link to site

https://directory.fsf.org/wiki/Libelf

Description

Libelf' lets you read, modify or create ELF files in an architecture-independent way.

Version

0.8.13

Usage instructions

module load libelf/0.8.13

Link to user guide/tutorial

http://www.mr511.de/software/libelf-0.8.13.README

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libevent

Software link to site

http://libevent.org/

Description

An event notification library

Version

2.1.8

Usage instructions

module load libevent/2.1.8

Link to user guide/tutorial

http://www.wangafu.net/~nickm/libevent-2.1/doxygen/html/

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Libfabric

Software link to site

https://ofiwg.github.io/libfabric/

Description

OpenFabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. Libfabric is a core component of OFI

Version

1.7.1

Usage instructions

module load libfabric

Link to user guide/tutorial

https://ofiwg.github.io/libfabric/

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Libffi

Software link to site

https://sourceware.org/libffi/

Description

None

Version

3.2.1

Usage instructions

module load libffi/3.2.1

Link to user guide/tutorial

https://sourceware.org/libffi/

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libfreeimage

Software link to site

http://freeimage.sourceforge.net/

Description

FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.

Version

3.18.0

Usage instructions

module load libfreeimage/3.18.0

Link to user guide/tutorial

http://freeimage.sourceforge.net/fip/index.html

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Libgc

Software link to site

https://github.com/ivmai/bdwgc

Description

Boehm-Demers-Weiser Garbage Collector - a conservative garbage collector for C and C++.

Version

7.6.0

Usage instructions

module load libgc/7.6.0

Link to user guide/tutorial

https://github.com/ivmai/bdwgc/wiki

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Libgd

Software link to site

https://libgd.github.io/

Description

GD is an open source code library for the dynamic creation of images by programmers.

Version

2.1.1, 2.2.1

Usage instructions

module load libgd/2.1.1 or module load libgd/2.2.1

Link to user guide/tutorial

https://libgd.github.io/manuals/2.1.1/files/preamble-txt.html

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libgpuarray

Software link to site

https://github.com/Theano/libgpuarray

Description

Make a common GPU ndarray(n dimensional array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple tasks

Version

0.7.5

Usage instructions

module load libgpuarray

Link to user guide/tutorial

http://deeplearning.net/software/libgpuarray/

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Libjpeg

Software link to site

http://libjpeg.sourceforge.net/

Description

None

Version

6b, 9c

Usage instructions

module load libjpeg/6b or module load libjpeg/9c

Link to user guide/tutorial

http://www.faqs.org/faqs/jpeg-faq/

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Libmatheval

Software link to site

https://www.gnu.org/software/libmatheval/

Description

A library which contains several procedures that make it possible to create an in-memory tree from the string representation of a mathematical function over single or multiple variables.

Version

1.1.11

Usage instructions

module load libmatheval/1.1.11

Link to user guide/tutorial

https://www.gnu.org/software/libmatheval/manual/libmatheval.html

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libmaus2

Software link to site

https://github.com/gt1/libmaus2

Description

a collection of data structures and algorithms - needed for other software modules

Version

2.0.344

Usage instructions

module load libmaus2

Link to user guide/tutorial

https://github.com/gt1/libmaus2

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Libmng

Software link to site

http://www.libpng.org/pub/mng/

Description

None

Version

2.0.2

Usage instructions

module load libmng/2.0.2

Link to user guide/tutorial

http://www.libpng.org/pub/mng/mngdocs.html

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Libpng

Software link to site

http://www.libpng.org/pub/png/libpng.html

Description

None

Version

1.6.16

Usage instructions

module load libpng/1.6.16

Link to user guide/tutorial

http://www.libpng.org/pub/png/libpng-1.4.0-manual.pdf

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libQGLViewer

Software link to site

http://libqglviewer.com/

Description

libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers.

Version

2.6.3, 2.7.1

Usage instructions

module load libqglviewer/xxx (where xxx is the version)

Link to user guide/tutorial

http://libqglviewer.com/refManual/hierarchy.html

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Libsodium

Software link to site

https://download.libsodium.org/doc/

Description

Sodium Cryptography library.

Version

1.0.6

Usage instructions

module load libsodium/1.0.6

Link to user guide/tutorial

https://download.libsodium.org/doc/

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libspatialindex

Software link to site

https://libspatialindex.github.io/

Description

An extensible framework that will support robust spatial indexing methods.

Version

2.6.3, 2.7.1

Usage instructions

module load libqglviewer/xxx (where xxx is the version)

Link to user guide/tutorial

http://libqglviewer.com/refManual/hierarchy.html

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Libspatialite

Software link to site

https://www.gaia-gis.it/fossil/libspatialite/index

Description

An open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.

Version

4.3.0

Usage instructions

module load libspatialite/4.3.0

Link to user guide/tutorial

https://www.gaia-gis.it/fossil/libspatialite/wiki

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Libspectre

Software link to site

https://www.freedesktop.org/wiki/Software/libspectre/

Description

None

Version

0.2.7

Usage instructions

module load libspectre/0.2.7

Link to user guide/tutorial

https://libspectre.freedesktop.org/manual/

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Libtau

Software link to site

https://integrativemodeling.org/libTAU.html

Description

None

Version

1.0.1

Usage instructions

module load libtau/1.0.1

Link to user guide/tutorial

https://integrativemodeling.org/doc.html

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Libtiff

Software link to site

http://www.libtiff.org/

Description

None

Version

4.0.3

Usage instructions

module load libtiff/4.0.3

Link to user guide/tutorial

http://www.libtiff.org/document.html

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Libtool

Software link to site

https://www.gnu.org/software/libtool/libtool.html

Description

None

Version

2.4.5

Usage instructions

module load libtool/2.4.5

Link to user guide/tutorial

https://www.gnu.org/software/libtool/manual/

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Libunistring

Software link to site

https://www.gnu.org/software/libunistring/

Description

This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

Version

0.9.7

Usage instructions

module load libunistring/0.9.7

Link to user guide/tutorial

https://www.gnu.org/software/libunistring/manual/libunistring.html

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Libxml2

Software link to site

http://xmlsoft.org/

Description

None

Version

2.9.2

Usage instructions

module load libxml2/2.9.2

Link to user guide/tutorial

http://xmlsoft.org/html/index.html

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Libxslt

Software link to site

http://xmlsoft.org/libxslt/

Description

None

Version

1.1.28

Usage instructions

module load libxslt/1.1.28

Link to user guide/tutorial

http://xmlsoft.org/libxslt/docs.html

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LIGGGHTS-PUBLIC

Software link to site

https://www.cfdem.com/media/DEM/docu/Manual.html

Description

An open source discrete element method particle simulation program.

Version

3.7.0, 3.8.0

Usage instructions

module load liggghts-public/3.7.0 or module load liggghts-public/3.8.0

Link to user guide/tutorial

https://www.cfdem.com/media/DEM/docu/Manual.html

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LIGGGHTS-with-bonds

Software link to site

https://github.com/richti83/LIGGGHTS-WITH-BONDS

Description

LIGGGHTS DEM software with Bonds enabled. This offering is not approved or endorsed by DCS Computing GmbH, the producer of the LIGGGHTS and CFDEMcoupling software and owner of the LIGGGHTS and CFDEM trade marks.

Version

3.3.0

Usage instructions

module load liggghts-with-bonds/3.3.0

Link to user guide/tutorial

https://github.com/richti83/LIGGGHTS-WITH-BONDS

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lighter

Software link to site

https://github.com/mourisl/Lighter

Description

Lighter is a kmer-based error correction method for whole genome sequencing data.

Version

1.1.1

Usage instructions

module load lighter

Link to user guide/tutorial

https://github.com/mourisl/Lighter

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Lmdb

Software link to site

http://www.lmdb.tech/doc/

Description

Symas Lightning Memory-Mapped Database (LMDB).

Version

0.9.7

Usage instructions

module load lmdb/0.9.7

Link to user guide/tutorial

http://www.lmdb.tech/doc/starting.html

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Lofreq

Software link to site

http://csb5.github.io/lofreq/

Description

LoFreq-star is a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.

Version

2.1.2

Usage instructions

module load lofreq/2.1.2

Link to user guide/tutorial

http://csb5.github.io/lofreq/commands/

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Loki

Software link to site

https://github.com/claudiordgz/Loki

Description

A C++ library of designs, containing flexible implementations of common design patterns and idioms.

Version

0.1.7

Usage instructions

module load loki/0.1.7

Link to user guide/tutorial

http://libqglviewer.com/refManual/hierarchy.html

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longranger

Software link to site

https://support.10xgenomics.com/genome-exome/software/downloads/latest

Description

Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.

Version

2.1.3

Usage instructions

module load longranger

Link to user guide/tutorial

https://support.10xgenomics.com/genome-exome/software/downloads/latest

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lordec

Software link to site

http://www.atgc-montpellier.fr/lordec/

Description

LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.

Version

0.6

Usage instructions

module load lordec

Link to user guide/tutorial

http://www.atgc-montpellier.fr/lordec/

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LS-DYNA

Software link to site

http://www.lstc.com/products/ls-dyna

Description

An advanced general-purpose multiphysics simulation software package developed by the Livermore Software Technology Corporation (LSTC).

Version

8.0.0, 8.0.0-intelmpi, 9.1.0, 9.1.0-intelmpi, 10.1.0, 10.1.0-intelmpi

Usage instructions

module load ls-dyna/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.lstc.com/download/manuals

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LS-PrePost

Software link to site

http://www.lstc.com/lspp/

Description

LS-DYNA Pre Post program.

Version

4.3, 4.5

Usage instructions

module load lsprepost/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.lstc.com/lspp/content/tutorials.shtml

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Lsd

Software link to site

http://www.atgc-montpellier.fr/LSD/

Description

LSD Fast dating using least-squares criteria and algorithms.

Version

0.2, 0.3

Usage instructions

module load lsd/0.2 or module load lsd/0.3

Link to user guide/tutorial

http://www.atgc-montpellier.fr/LSD/

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Lua

Software link to site

https://www.lua.org/

Description

Lua is a powerful, fast, lightweight, embeddable scripting language.

Version

5.1.5, 5.2.4, 5.3.1

Usage instructions

module load lua/xxx (where xxx represents version number)

Link to user guide/tutorial

https://www.lua.org/docs.html

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Luabind

Software link to site

http://www.rasterbar.com/products/luabind.html

Description

A library that helps you create bindings between C++ and Lua.

Version

0.9.1

Usage instructions

module load luabind/0.9.1

Link to user guide/tutorial

http://www.rasterbar.com/products/luabind/docs.html

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Luajit

Software link to site

http://luajit.org/

Description

LuaJit is a Just-In-Time Compiler (JIT) for the lua programming language.

Version

2.0.4

Usage instructions

module load luajit/2.0.4

Link to user guide/tutorial

http://wiki.luajit.org/Home

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lumpy-sv

Software link to site

https://github.com/arq5x/lumpy-sv

Description

Lumpy: a general probabilistic framework for structural variant discovery.

Version

0.2.11, 0.2.12, 0.2.13

Usage instructions

module load lumpy-sv/xxx (where xxx represents version number)

Link to user guide/tutorial

https://github.com/arq5x/lumpy-sv

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Lzma

Software link to site

http://tukaani.org/lzma/

Description

LZMA Utils are legacy data compression software with high compression ratio.

Version

4.32.7

Usage instructions

module load lzma/4.32.7

Link to user guide/tutorial

https://sourceforge.net/p/lzmautils/discussion/708858

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M4

Software link to site

https://www.gnu.org/software/m4/m4.html

Description

GNU M4 is an implementation of the traditional Unix macro processor.

Version

1.4.17

Usage instructions

module load m4/1.4.17

Link to user guide/tutorial

https://www.gnu.org/software/m4/manual/index.html

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Macaulay2

Software link to site

https://faculty.math.illinois.edu/Macaulay2/

Description

Macaulay2 is a software system devoted to supporting research in algebraic geometry and commutative algebra.

Version

1.9.2.1

Usage instructions

module load macalay2

Link to user guide/tutorial

https://faculty.math.illinois.edu/Macaulay2/doc/Macaulay2-1.10/share/doc/Macaulay2/Macaulay2Doc/html/

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MACH

Software link to site

http://csg.sph.umich.edu/abecasis/mach/

Description

MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Version

1.0.18.c

Usage instructions

module load mach/1.0.18.c

Link to user guide/tutorial

http://csg.sph.umich.edu/abecasis/mach/tour/

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MaCH-Admix

Software link to site

http://www.unc.edu/~yunmli/MaCH-Admix/

Description

MaCH-Admix is a genotype imputation software that extends the capabilities of MaCH 1.0

Version

2.0.203

Usage instructions

module load mach-admix/2.0.203

Link to user guide/tutorial

http://www.unc.edu/~yunmli/MaCH-Admix/tutorial.php

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Macs

Software link to site

http://liulab.dfci.harvard.edu/MACS/

Description

MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.

Version

2.1.0

Usage instructions

module load macs/2.1.0

Link to user guide/tutorial

http://liulab.dfci.harvard.edu/MACS/README.html

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MAFFT

Software link to site

http://mafft.cbrc.jp/alignment/software/

Description

Multiple alignment program for amino acid or nucleotide sequences.

Version

7.300, 7.402

Usage instructions

module load mafft/xxx (replace xxx with the version you want)

Link to user guide/tutorial

http://mafft.cbrc.jp/alignment/software/tips0.html

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Magic-BLAST

Software link to site

https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST/

Description

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.

Version

1.3.0

Usage instructions

module load magicblast

Link to user guide/tutorial

https://github.com/ncbi/sra-tools/wiki/Downloads

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Maker

Software link to site

http://www.yandell-lab.org/software/maker.html

Description

MAKER is a portable and easily configurable genome annotation pipeline.

Version

2.31.8, 2.31.10

Usage instructions

module load maker/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.yandell-lab.org/software/maker.html

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Manta

Software link to site

https://github.com/Illumina/manta

Description

Structural variant and indel caller for mapped sequencing data

Version

1.4.0

Usage instructions

module load manta/1.4.0

Link to user guide/tutorial

https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md

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MARVEL

Software link to site

https://github.com/schloi/MARVEL

Description

MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.

Version

36d78a9

Usage instructions

module load marvel/36d78a9

Link to user guide/tutorial

https://github.com/schloi/MARVEL

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Mash

Software link to site

https://github.com/marbl/Mash

Description

Fast genome and metagenome distance estimation using MinHash

Version

2, 2.1

Usage instructions

module load mash/xxx (where xxx is the version)

Link to user guide/tutorial

http://mash.readthedocs.io/en/latest/

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MATAM

Software link to site

https://github.com/bonsai-team/matam

Description

Mapping-Assisted Targeted-Assembly for Metagenomics - TESTING ONLY

Version

1

Usage instructions

module load matam

Link to user guide/tutorial

https://github.com/bonsai-team/matam

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Mathematica

Software link to site

https://www.wolfram.com/mathematica/

Description

Mathematica - system for technical computing.

Version

11.1.1

Usage instructions

module load mathematica/11.1.1

Link to user guide/tutorial

https://www.wolfram.com/mathematica/resources/

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MathGL

Software link to site

https://sourceforge.net/projects/mathgl/

Description

A free cross-platform library of fast C++ routines for the plotting of up to 3-ranged data.

Version

1.11.3, 2.4.2.1

Usage instructions

module load mathgl/xxx (where xxx is the version)

Link to user guide/tutorial

https://sourceforge.net/projects/mathgl/files/mathgl/mathgl%202.4.2/mgl-2.4.2.1.eng.pdf/download

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Matlab

Software link to site

https://au.mathworks.com/products/matlab.html

Description

Numerical computing environment allowing matrix manipulation, plotting of functions and data. To learn how to submit Matlab jobs to Artemis from your desktop, see

https://rc.sydney.edu.au/matlab-gateway/


Version

R2013a, R2014b, R2015b, R2016b, R2017a, R2017b, R2018a, R2018b, R2019a

Usage instructions

module load matlab/xxx (where xxx represents version number)

Link to user guide/tutorial

https://matlabacademy.mathworks.com/

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Mauve

Software link to site

http://darlinglab.org/mauve/mauve.html

Description

MAUVE is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

Version

2.4.0

Usage instructions

module load mauve/2.4.0

Link to user guide/tutorial

http://darlinglab.org/mauve/user-guide/introduction.html

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Maven

Software link to site

https://maven.apache.org/

Description

Apache Maven is a software project management and comprehension tool.

Version

3.5.2

Usage instructions

module load maven/3.5.2

Link to user guide/tutorial

https://maven.apache.org/

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Mawk

Software link to site

http://invisible-island.net/mawk/mawk.html

Description

mawkis an interpreter for the AWK Programming Language.

Version

1.3.4

Usage instructions

module load mawk/1.3.4

Link to user guide/tutorial

http://invisible-island.net/mawk/mawk.html#documentation

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MaxBin2

Software link to site

https://sourceforge.net/projects/maxbin2/

Description

MaxBin clusters metagenomic contigs into different bins, each consists of contigs from one species.

Version

2.2.6

Usage instructions

module load maxbin2

Link to user guide/tutorial

https://sourceforge.net/projects/maxbin2/

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MayaVi

Software link to site

http://mayavi.sourceforge.net/download.html

Description

Mayavi 3D scientific data visualization and plotting in Python

Version

4.5

Usage instructions

module load mayavi

Link to user guide/tutorial

http://mayavi.sourceforge.net/docs.html

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Mcl

Software link to site

http://micans.org/mcl/

Description

The MCL algorithm is short for the Markov Cluster Algorithm.

Version

14-137

Usage instructions

module load mcl/14-137

Link to user guide/tutorial

http://micans.org/mcl/

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MCR

Software link to site

https://au.mathworks.com/products/compiler/mcr.html

Description

Matlab compiler runtimes

Version

R2013a, R2014a, R2014b, R2016a, R2016b, R2017a

Usage instructions

module load mcr/xxx (where xxx is the version)

Link to user guide/tutorial

https://au.mathworks.com/help/compiler/deployment-process.html

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Medusa

Software link to site

https://github.com/combogenomics/medusa

Description

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

Version

1.6

Usage instructions

module load medusa/1.6

Link to user guide/tutorial

https://github.com/combogenomics/medusa

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Megacc

Software link to site

http://www.megasoftware.net/

Description

Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations.

Version

7.0.14-1

Usage instructions

module load megacc/7.0.14-1

Link to user guide/tutorial

http://www.megasoftware.net/web_help_7/helpfile.htm#hc_first_time_user.htm

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Megahit

Software link to site

https://github.com/voutcn/megahit

Description

An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.

Version

1.0.6.1, 1.1.2, 1.1.3

Usage instructions

module load megahit/xxx (replace xxx with the version you want)

Link to user guide/tutorial

https://github.com/voutcn/megahit/wiki

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megan

Software link to site

http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html

Description

MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. (Community Version)

Version

6.8.13

Usage instructions

module load megan

Link to user guide/tutorial

http://ab.inf.uni-tuebingen.de/data/software/megan6/download/welcome.html

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MELT

Software link to site

http://melt.igs.umaryland.edu/

Description

The Mobile Element Locator Tool (MELT) is a software package, written in Java, that discovers, annotates, and genotypes non-reference Mobile Element Insertions (MEIs) in Illumina DNA paired-end whole genome sequencing (WGS) data.

Version

2.1.5

Usage instructions

module load melt/2.1.5

Link to user guide/tutorial

http://melt.igs.umaryland.edu/manual.php

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Meme

Software link to site

http://meme-suite.org/

Description

The MEME Suite Motif-based sequence analysis tools.

Version

4.11.2_2, 4.11.3_1

Usage instructions

module load meme/4.11.2_2 or module load meme/4.11.3_1

Link to user guide/tutorial

http://meme-suite.org/doc/overview.html?man_type=web

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Mercurial

Software link to site

https://www.mercurial-scm.org/

Description

Mercurial is a free, distributed source control management tool.

Version

3.8.3

Usage instructions

module load mercurial/3.8.3

Link to user guide/tutorial

https://www.mercurial-scm.org/guide

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MetaBAT

Software link to site

https://bitbucket.org/berkeleylab/metabat/src/master/

Description

MetaBAT: A robust statistical framework for reconstructing genomes from metagenomic data

Version

2.12.1

Usage instructions

module load metabat

Link to user guide/tutorial

https://bitbucket.org/berkeleylab/metabat/src/master/

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MetaPhlAn2

Software link to site

http://huttenhower.sph.harvard.edu/metaphlan2

Description

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

Version

2.6.0

Usage instructions

module load metaphlan2/2.6.0

Link to user guide/tutorial

https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2

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MetaSim

Software link to site

https://ab.inf.uni-tuebingen.de/software/metasim

Description

A Sequencing Simulator for Genomics and Metagenomics.

Version

0.9.5

Usage instructions

module load metasim

Link to user guide/tutorial

https://ab.inf.uni-tuebingen.de/software/metasim

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Metatissue

Software link to site

http://genetics.cs.ucla.edu/metatissue/

Description

Meta-analysis for multi-tissue eQTL studies.

Version

0.4

Usage instructions

module load metatissue/0.4

Link to user guide/tutorial

http://genetics.cs.ucla.edu/metatissue/faq.html

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MetaVelvet

Software link to site

http://metavelvet.dna.bio.keio.ac.jp/

Description

An extension of Velvet assembler to de novo metagenomic assembly

Version

1.2.02

Usage instructions

module load metavelvet

Link to user guide/tutorial

http://metavelvet.dna.bio.keio.ac.jp/

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meth_progs

Software link to site

https://www.otago.ac.nz/cs/groups/public/@biochemistry/documents/webcontent/otago644426.gz

Description

Programs and Scripts for Bisulphite Sequence Data

Version

2017

Usage instructions

module load methprogs

Link to user guide/tutorial


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Methpipe

Software link to site

http://smithlabresearch.org/downloads/methpipe-3.4.3.tar.bz2

Description

MethPipe - a computational pipeline for analyzing bisulfite sequencing

Version

3.4.3

Usage instructions

module load methpipe

Link to user guide/tutorial

http://smithlabresearch.org/software/methpipe/

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MethylDackel

Software link to site

https://github.com/dpryan79/methyldackel

Description

A (mostly) universal methylation extractor for BS-seq experiments.

Version

0.3.0

Usage instructions

module load methyldackel/0.3.0

Link to user guide/tutorial

https://github.com/dpryan79/methyldackel

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METIS

Software link to site

http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

Description

Serial Graph Partitioning and Fill-reducing Matrix Ordering

Version

5.1.0

Usage instructions

module load metis/5.1.0

Link to user guide/tutorial

http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/manual.pdf

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Migrate-N

Software link to site

http://popgen.sc.fsu.edu/Migrate/Migrate-n.html

Description

Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes.

Version

3.6.11

Usage instructions

module load migrate-n/3.6.11

Link to user guide/tutorial

http://popgen.sc.fsu.edu/Migrate/Tutorials/Tutorials.html

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minced

Software link to site

https://github.com/ctSkennerton/minced

Description

Mining CRISPRs in Environmental Datasets

Version

0.2.0, 0.3.3

Usage instructions

module load minced/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/ctSkennerton/minced

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Minimac2

Software link to site

https://genome.sph.umich.edu/wiki/Minimac

Description

A low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation

Version

2014.9.15

Usage instructions

module load minimac2

Link to user guide/tutorial

https://genome.sph.umich.edu/wiki/Minimac

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Minimac4

Software link to site

https://genome.sph.umich.edu/wiki/Minimac

Description

A low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation

Version

1.0.1

Usage instructions

module load minimac4

Link to user guide/tutorial

https://genome.sph.umich.edu/wiki/Minimac

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Minimap2

Software link to site

https://github.com/lh3/minimap2

Description

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

Version

2.3

Usage instructions

module load minimap/2.3

Link to user guide/tutorial

https://github.com/lh3/minimap2#users-guide

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MIPAV

Software link to site

https://mipav.cit.nih.gov/

Description

The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities

Version

7.4.0

Usage instructions

module load mipav

Link to user guide/tutorial

https://mipav.cit.nih.gov/

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Mira

Software link to site

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

Description

MIRA is a multi-pass DNA sequence data assembler.

Version

4.0.2

Usage instructions

module load mira/4.0.2

Link to user guide/tutorial

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html

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Mirdeep2

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MISTReSS

Software link to site

https://github.com/Papos92/MISTReSS

Description

MLVA In Silico Typing Resource for Salmonella Strains

Version

1

Usage instructions

module load mistress/1

Link to user guide/tutorial

http://gmsh.info/doc/texinfo/gmsh.html

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Mlst

Software link to site

http://www.mlst.net/

Description

Scan contig files against PubMLST typing schemes.

Version

2.6, 2.8, 2.15.1

Usage instructions

module load mlst/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.mlst.net/

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Modeller

Software link to site

https://salilab.org/modeller/

Description

None

Version

9.15

Usage instructions

module load modeller/9.15

Link to user guide/tutorial

https://salilab.org/modeller/manual/

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Molpro

Software link to site

http://www.molpro.net/info/users?portal=user

Description

Quantum Chemistry Software.

Version

2015-gcc-mpi, 2015-gcc-mpi-test2, 2015-intel-mpi

Usage instructions

module load molpro/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.molpro.net/info/2015.1/doc/manual/index.html?portal=user&choice=User%27s+manual

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MongoDB

Software link to site

https://www.mongodb.com/

Description

MongoDB is a document database

Version

4.0.4

Usage instructions

module load mongodb/4.0.4

Link to user guide/tutorial

https://docs.mongodb.com/

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Mono

Software link to site

https://www.mono-project.com/

Description

Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.

Version

5.12.0.301

Usage instructions

module load mono

Link to user guide/tutorial

https://www.mono-project.com/docs/

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Mothur

Software link to site

https://www.mothur.org/

Description

A single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

Version

1.36.1, 1.38.1

Usage instructions

module load mothur/1.36.1 or module load mothur/1.38.1

Link to user guide/tutorial

https://mothur.org/wiki/Main_Page

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MPC

Software link to site

http://www.multiprecision.org/mpc/

Description

C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result.

Version

0.8.1,1.0.3, 1.1.0

Usage instructions

module load mpc/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.multiprecision.org/mpc/documentation.html

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MPFR

Software link to site

http://www.mpfr.org/

Description

C library for multiple-precision floating-point computations with correct rounding.

Version

2.4.2, 3.1.4, 4.0.2

Usage instructions

module load mpfr/2.4.2 or module load mpfr/3.1.4

Link to user guide/tutorial

http://www.mpfr.org/mpfr-current/#doc

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mpiBWA

Software link to site

https://github.com/fredjarlier/mpiBWA

Description

Scalable mpi aligner base on BWA

Version

1

Usage instructions

module load mpibwa/1

Link to user guide/tutorial

https://github.com/fredjarlier/mpiBWA

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Mpich

Software link to site

https://www.mpich.org/

Description

MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).

Version

3.2, 3.2-intel

Usage instructions

module load mpich/3.2 or module load mpich/3.2-intel

Link to user guide/tutorial

https://www.mpich.org/documentation/guides/

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Mrbayes

Software link to site

http://mrbayes.sourceforge.net/

Description

A program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Version

3.2.5

Usage instructions

module load mrbayes/3.2.5

Link to user guide/tutorial

http://mrbayes.sourceforge.net/manual.php

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MRtrix3

Software link to site

http://www.mrtrix.org/

Description

Serial Graph Partitioning and Fill-reducing Matrix Ordering

Version

3.0_RC3, 3.0

Usage instructions

module load mrtrix3/xxx (where xxx is the version)

Link to user guide/tutorial

https://mrtrix.readthedocs.io/en/latest/

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MTBseq

Software link to site

https://github.com/ngs-fzb/MTBseq_source

Description

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Version

1

Usage instructions

module load mtbseq

Link to user guide/tutorial

https://github.com/ngs-fzb/MTBseq_source/blob/master/README.pdf

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Mugsy

Software link to site

http://mugsy.sourceforge.net/

Description

Mugsy - multiple whole genome alignment tool.

Version

2.3

Usage instructions

module load mugsy/2.3

Link to user guide/tutorial

http://mugsy.sourceforge.net/#started

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Mummer3

Software link to site

http://mummer.sourceforge.net/

Description

A modular system for the rapid whole genome alignment of finished or draft sequences.

Version

3.23

Usage instructions

module load mummer3

Link to user guide/tutorial

http://mummer.sourceforge.net/manual/

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Mummer4

Software link to site

https://github.com/mummer4/mummer

Description

Mummer alignment tool

Version

4.0.0beta2

Usage instructions

module load mummer4

Link to user guide/tutorial

https://github.com/mummer4/mummer

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Mutect

Software link to site

http://archive.broadinstitute.org/cancer/cga/mutect

Description

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Version

1.1.4

Usage instructions

module load mutect/1.1.4

Link to user guide/tutorial

http://gatkforums.broadinstitute.org/gatk/categories/mutect-documentation

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MVAPICH2

Software link to site

http://mvapich.cse.ohio-state.edu/

Description

MVAPICH: MPI over InfiniBand, Omni-Path, Ethernet.

Version

2.3-intel

Usage instructions

module load mvapich2/2.3-intel

Link to user guide/tutorial

http://mvapich.cse.ohio-state.edu/userguide/

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MXNet

Software link to site

http://mxnet.io/

Description

A deep learning framework.

Version

0.7.0, 1.0.0, 1.4.0

Usage instructions

module load mxnet/xxx (where xxx is the version)

Link to user guide/tutorial

http://mxnet.io/tutorials/index.html

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Mykrobe-Predictor

Software link to site

http://www.mykrobe.com/products/predictor/

Description

Antibiotic resistance predictions.

Version

0.3.6, master

Usage instructions

module load mykrobe-predictor/0.3.6 or module load mykrobe-predictor/master

Link to user guide/tutorial

http://www.mykrobe.com/products/predictor/

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MySQL

Software link to site

https://www.mysql.com/

Description

MySQL clients. You can't run a database server on Artemis.

Version

5.7.1

Usage instructions

module load mysql/5.7.1

Link to user guide/tutorial

https://dev.mysql.com/doc/

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NAMD

Software link to site

http://www.ks.uiuc.edu/Research/namd/

Description

Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

Version

2.106openmpi-gcc,2.11-cuda, 2.11-openmpi-gcc, 2.11-intel-mpi, 2.13-cuda, 2.13-intel-mpi

Usage instructions

module load namd/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.ks.uiuc.edu/Training/Tutorials/#namd

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NanoOk

Software link to site

https://nanoporetech.com/resource-centre/publications/nanook-flexible-multi-reference-software-pre-and-post-alignment

Description

Flexible, multi-reference software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles.

Version

1.31

Usage instructions

module load nanook/1.31

Link to user guide/tutorial

https://documentation.tgac.ac.uk/display/NANOOK/NanoOK

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Nanopolish

Software link to site

https://github.com/jts/nanopolish

Description

Software package for signal-level analysis of Oxford Nanopore sequencing data.

Version

0.8.4

Usage instructions

module load nanopolish/0.8.4

Link to user guide/tutorial

https://github.com/jts/nanopolish

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NASM

Software link to site

https://www.nasm.us/

Description

NASM is an assembler and disassembler for the Intel x86 architecture

Version

2.14.02

Usage instructions

module load nasm/2.14.02

Link to user guide/tutorial

https://www.nasm.us/docs.php

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Nastran

Software link to site

https://github.com/nasa/NASTRAN-95

Description

Nastran is the NASA Structural Analysis System, a finite element analysis program.

Version

95

Usage instructions

module load nastran/95

Link to user guide/tutorial

https://github.com/nasa/NASTRAN-95/blob/master/NASTRAN%20Users%20Manual%202.pdf

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NCBI C++ Toolkit

Software link to site

https://www.ncbi.nlm.nih.gov/toolkit

Description

A public-domain collection of portable libraries, consisting of a cross-platform application framework and a set of utilities and supporting classes to work with biological data.

Version

21.0.0

Usage instructions

module load ncbi-cxx/21.0.0

Link to user guide/tutorial

http://www.unc.edu/~yunmli/MaCH-Admix/tutorial.php

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Ncurses

Software link to site

https://www.gnu.org/software/ncurses/

Description

Ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.

Version

5.9, 6

Usage instructions

module load ncurses/5.9 or module load ncurses/6

Link to user guide/tutorial

https://www.gnu.org/software/ncurses/

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Ncview

Software link to site

http://meteora.ucsd.edu/~pierce/ncview_home_page.html

Description

A netCDF visual browser

Version

2.1.7

Usage instructions

module load ncview

Link to user guide/tutorial

http://meteora.ucsd.edu/~pierce/docs/ncview.README

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NetCDF

Software link to site

http://www.unidata.ucar.edu/software/netcdf/

Description

NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Version

4.4.0, 4.4.1.1, 4.4.3, 4.4.4, 4.6.1

Usage instructions

Type module avail netcdf on Artemis to see all available versions

Link to user guide/tutorial

http://www.unidata.ucar.edu/software/netcdf/docs/user_guide.html

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Netgen

Software link to site

https://sourceforge.net/projects/netgen-mesher/

Description

Netgen Mesh Generator NETGEN is an automatic 3d tetrahedral mesh generator.

Version

6.1-dev

Usage instructions

module load netgen/6.1-dev

Link to user guide/tutorial

https://sourceforge.net/p/netgen-mesher/wiki/Home/

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Netlogo

Software link to site

https://ccl.northwestern.edu/netlogo/

Description

NetLogo is a multi-agent programmable modeling environment.

Version

5.2.1, 5.3.1, 6.0.2

Usage instructions

module load netlogo/xxx (where xxx is the version number)

Link to user guide/tutorial

https://ccl.northwestern.edu/netlogo/docs/NetLogo%20User%20Manual.pdf

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Nettle

Software link to site

https://directory.fsf.org/wiki/Nettle

Description

A cryptographic library that is designed to fit easily in more or less any context.

Version

3.2

Usage instructions

module load nettle/3.2

Link to user guide/tutorial

http://www.lysator.liu.se/~nisse/nettle/nettle.html

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Newick-Utils

Software link to site

http://cegg.unige.ch/newick_utils

Description

The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees.

Version

1.6

Usage instructions

module load newick-utils/1.6

Link to user guide/tutorial

http://cegg.unige.ch/pub/nwutils_tutorial-1.6.pdf

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Nextflow

Software link to site

https://www.nextflow.io/

Description

Data-driven computational pipelines.

Version

0.22.1, 0.30.2

Usage instructions

module load nextflow/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.nextflow.io/docs/latest/index.html

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nim

Software link to site

https://nim-lang.org/

Description

Nim is a systems and applications programming language.

Version

0.18.0

Usage instructions

module load nim/0.18.0

Link to user guide/tutorial

https://nim-lang.org/documentation.html

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Nlopt

Software link to site

http://ab-initio.mit.edu/wiki/index.php/Nlopt

Description

NLoptis a free/open-source library fornonlinear optimisation.

Version

2.4.2

Usage instructions

module load nlopt/2.4.2

Link to user guide/tutorial

http://ab-initio.mit.edu/wiki/index.php/NLopt_manual

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Node

Software link to site

https://www.npmjs.com/

Description

Node for npm.

Version

5.0.0

Usage instructions

module load node/5.0.0

Link to user guide/tutorial

https://docs.npmjs.com/

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Norgal

Software link to site

https://bitbucket.org/kosaidtu/norgal

Description

Norgal takes NGS sequencing reads as input (currently only Illumina paired end reads are supported) and tries to assemble the mitochondrial genome using kmer frequencies.

Version

1.0.0

Usage instructions

module load norgal

Link to user guide/tutorial

https://bitbucket.org/kosaidtu/norgal

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Nullarbor

Software link to site

https://github.com/tseemann/nullarbor

Description

Pipeline to generate complete public health microbiology reports from sequenced isolates.

Version

1.01, 1.20, 1.41, 2.0, 2.0.20181010.b9b2d41

Usage instructions

module load nullarbor/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/tseemann/nullarbor

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oases

Software link to site

https://github.com/dzerbino/oases

Description

De novo transcriptome assembler for short reads

Version

0.2.09

Usage instructions

module load oases

Link to user guide/tutorial

https://github.com/dzerbino/oases

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Octave

Software link to site

https://www.gnu.org/software/octave/

Description

High-level language, primarily intended for numerical computations and is highly compatiable with MATLAB.

Version

3.8.2

Usage instructions

module load octave/3.8.2

Link to user guide/tutorial

https://www.gnu.org/software/octave/doc/interpreter/

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ODE

Software link to site

https://www.ode.org/

Description

ODE is an open source, high performance library for simulating rigid body dynamics

Version

0.16

Usage instructions

module load ode

Link to user guide/tutorial

https://www.ode.org/

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OmegaPlus

Software link to site

https://github.com/alachins/omegaplus

Description

A scalable tool for rapid detection of selective sweeps in whole-genome datasets

Version

2.2.5

Usage instructions

module load omegaplus/2.2.5

Link to user guide/tutorial

https://github.com/alachins/omegaplus

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OpenBLAS

Software link to site

http://www.openblas.net/

Description

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

Version

0.2.14, 0.2.18, 0.3.4

Usage instructions

module load openblas/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.openblas.net/

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OpenCV

Software link to site

http://opencv.org/

Description

OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.

Version

2.4.11, 3.4.0

Usage instructions

module load opencv/2.4.11 or module load opencv/3.4.0

Link to user guide/tutorial

https://docs.opencv.org/

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OpenFOAM

Software link to site

https://www.openfoam.com/

Description

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Version

2.3.1, 2.4.0, 3.0.1, 3.0.1-intel, 3.0.x, 4.0, foam-extend-4.0, 4.1, 4.1-intel, 5.0, v1612+, v1712, 6, 7

Usage instructions

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.

Link to user guide/tutorial

https://sourceforge.net/projects/openfoamplus/files/v1612%2B/UserGuide.pdf/download

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OpenJPEG

Software link to site

http://www.openjpeg.org/

Description

None

Version

2.1.0

Usage instructions

module load openjpeg/2.1.0

Link to user guide/tutorial

https://github.com/uclouvain/openjpeg/wiki/Installation

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OpenMPI-gcc

Software link to site

https://www.open-mpi.org/

Description

Open source implementation of the MPI-3 message passing protocol for parallel computations. Compiled with gcc.

Version

1.8.4, 1.10.3, 2.1.2, 3.0.0, 3.0.0-64, 3.0.0-cuda, 3.0.1, 3.1.3, 3.1.3-cuda10, 4.0.0-cuda10

Usage instructions

Type module avail openmpi on Artemis to see all available versions

Link to user guide/tutorial

https://www.open-mpi.org/doc/

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OpenMPI-Intel

Software link to site

https://www.open-mpi.org/

Description

Open source implementation of the MPI-3 message passing protocol for parallel computations. Compiled with Intel compilers.

Version

1.8.4, 1.8.7, 1.10.3, 3.0.0, 3.1.3

Usage instructions

module load openmpi-intel/xxx (where xxx represents the version number)

Link to user guide/tutorial

https://www.open-mpi.org/doc/

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OpenMPI-PGI

Software link to site

https://www.open-mpi.org/

Description

Open source implementation of the MPI-2 message passing protocol for parallel computations. Compiled with PGI compilers.

Version

1.8.4

Usage instructions

module load openmpi-pgi/1.8.4

Link to user guide/tutorial

https://www.open-mpi.org/doc/

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OpenSlide

Software link to site

https://openslide.org/

Description

OpenSlide is a C library that provides a simple interface to read whole-slide images

Version

3.4.1

Usage instructions

module load openslide

Link to user guide/tutorial

https://openslide.org/

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OpenSSL

Software link to site

https://www.openssl.org/

Description

OpenSSL is an open source project that provides a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library.

Version

1.0.1s, 1.0.1t, 1.1.0h

Usage instructions

module load openssl/xxx (where xxx is the version number)

Link to user guide/tutorial

https://www.openssl.org/docs/

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ORCA

Software link to site

https://orcaforum.kofo.mpg.de/

Description

An Ab Initio, DFT and Semiempirical electronic structure package

Version

4.1.1

Usage instructions

module load orca/4.1.1

Link to user guide/tutorial

https://orcaforum.kofo.mpg.de/

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OrthoFiller

Software link to site

https://github.com/mpdunne/orthofiller

Description

Identifying missing annotations for evolutionarily conserved genes.

Version

1.1.1

Usage instructions

module load orthofiller

Link to user guide/tutorial

https://github.com/mpdunne/orthofiller

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OrthoFinder

Software link to site

https://github.com/davidemms/OrthoFinder

Description

Accurate inference of orthologs, orthogroups, the rooted species, gene trees and gene duplcation events tree

Version

2.2.7

Usage instructions

module load orthofinder

Link to user guide/tutorial

https://github.com/davidemms/OrthoFinder

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Osrm

Software link to site

http://project-osrm.org/

Description

Opensource routing machine for shortest paths in road networks.

Version

4.8.1

Usage instructions

module load osrm/4.8.1

Link to user guide/tutorial

http://project-osrm.org/docs/v5.6.0/api/#general-options

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Paml

Software link to site

http://abacus.gene.ucl.ac.uk/software/paml.html

Description

A package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.

Version

4.8a

Usage instructions

module load paml/4.8a

Link to user guide/tutorial

http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf

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pandaseq

Software link to site

https://github.com/neufeld/pandaseq

Description

PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

Version

2.11

Usage instructions

module load pandaseq

Link to user guide/tutorial

https://github.com/neufeld/pandaseq

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Pandoc

Software link to site

https://pandoc.org/

Description

A universal document converter.

Version

1.17.0.3

Usage instructions

module load pandoc/1.17.0.3

Link to user guide/tutorial

https://pandoc.org/MANUAL.html

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Pango

Software link to site

http://www.pango.org/

Description

None

Version

1.36.8

Usage instructions

module load pango/1.36.8

Link to user guide/tutorial

https://developer.gnome.org/pango/unstable/

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Parallel

Software link to site

https://www.gnu.org/software/parallel/

Description

A shell tool for executing jobs in parallel using one or more computers.

Version

20160222

Usage instructions

module load parallel/20160222

Link to user guide/tutorial

https://www.gnu.org/manual/manual.html

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Paraview

Software link to site

https://www.paraview.org/

Description

ParaView is an open-source, multi-platform data analysis and visualization application.

Version

4.0.1, 4.4.0, 5.4.1, 5.6.0

Usage instructions

module load paraview/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.paraview.org/resources/

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Pblat

Software link to site

http://icebert.github.io/pblat/

Description

Parallelised blat.

Version

35

Usage instructions

module load pblat/35

Link to user guide/tutorial

http://icebert.github.io/pblat/

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Pcre

Software link to site

http://pcre.org/

Description

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Version

7.0, 8.39, 8.41

Usage instructions

module load pcre/xxx (where xxx is the version)

Link to user guide/tutorial

http://pcre.org/

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Pcre2

Software link to site

http://pcre.org/

Description

The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Version

10.00

Usage instructions

module load pcre2

Link to user guide/tutorial

http://pcre.org/

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Pear

Software link to site

http://sco.h-its.org/exelixis/web/software/pear/

Description

An ultrafast, memory-efficient and highly accurate pair-end read merger.

Version

0.9.6

Usage instructions

module load pear/0.9.6

Link to user guide/tutorial

http://sco.h-its.org/exelixis/web/software/pear/doc.html

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PennCNV

Software link to site

https://github.com/WGLab/PennCNV

Description

PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays.

Version

1.0.4

Usage instructions

module load penncnv

Link to user guide/tutorial

http://penncnv.openbioinformatics.org/en/latest/

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Perl

Software link to site

https://www.perl.org/

Description

Perl 5 is a highly capable, feature-rich programming language.

Version

5.20.1,5.24.0

Usage instructions

module load perl/5.20.1 or module load perl/5.24.0

Link to user guide/tutorial

https://www.perl.org/docs.html

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petsc

Software link to site

http://www.mcs.anl.gov/petsc/download/

Description

PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications.

Version

3.7.6, 3.8.4, 3.9.3

Usage instructions

To see all available versions, type "module avail petsc" on the Artemis command line.

Link to user guide/tutorial

http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf

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pgdspider

Software link to site

http://www.cmpg.unibe.ch/software/PGDSpider/

Description

An automated data conversion tool for connecting population genetics and genomics programs

Version

2.1.1.1

Usage instructions

module load pgdspider

Link to user guide/tutorial

http://www.cmpg.unibe.ch/software/PGDSpider/

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Pgi

Software link to site

http://www.pgroup.com/

Description

PGI compilers for Fortran, C and C++ from the Portland Group.

Version

14.10, 15.1, 18.1, 18.4

Usage instructions

module load pgi/xxx, where xxx is the version number

Link to user guide/tutorial

http://www.pgroup.com/resources/docs.php

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Pgsql

Software link to site

https://www.postgresql.org/

Description

PostgreSQL. Library use only. Not for general use.

Version

9.4.4,9.5.3

Usage instructions

module load pgsql/9.4.4 or module load pgsql/9.5.3

Link to user guide/tutorial

https://www.postgresql.org/docs/

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phase

Software link to site

http://stephenslab.uchicago.edu/phase/download.html

Description

PHASE - A program for reconstructing haplotypes from population data

Version

2.1.1

Usage instructions

module load phase

Link to user guide/tutorial

http://stephenslab.uchicago.edu/phase/download.html

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PHCpack

Software link to site

http://homepages.math.uic.edu/~jan/PHCpack/phcpack.html

Description

PHCpack a general-purpose solver for polynomial systems by homotopy continuation.

Version

2.4.36

Usage instructions

module load phcpack/2.4.36

Link to user guide/tutorial

http://homepages.math.uic.edu/~jan/PHCpack/phcpack.html

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Pheniqs

Software link to site

https://biosails.github.io/pheniqs/

Description

Pheniqs is a generic high throughput DNA sequence demultiplexer and quality analyzer written in multi threaded C++11.

Version

1.1.1

Usage instructions

module load pheniqs/1.1.1

Link to user guide/tutorial

https://biosails.github.io/pheniqs/manual.html

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Phobius

Software link to site

http://phobius.sbc.su.se/

Description

A hidden Markov Model capable of predicting both Transmembrane Topology and Signal peptides

Version

1.01

Usage instructions

module load phobius

Link to user guide/tutorial

http://phobius.sbc.su.se/instructions.html

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Photoscan-Pro

Software link to site

http://www.agisoft.com/

Description

Agisoft PhotoScan performs photogrammetric processing of digital images and generates 3D spatial data.

Version

1.1.6, 1.2.3

Usage instructions

module load photoscan-pro/1.1.6 or module load photoscan-pro/1.2.3

Link to user guide/tutorial

http://www.agisoft.com/support/tutorials/beginner-level/

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PHYLIP

Software link to site

https://github.com/WGLab/PennCNV

Description

PHYLIP is a free package of programs for inferring phylogenies.

Version

3.697

Usage instructions

module load phylip

Link to user guide/tutorial

http://evolution.genetics.washington.edu/phylip/phylip.html

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PhyloBayes

Software link to site

http://www.atgc-montpellier.fr/phylobayes/

Description

Bayesian phylogenetic software based on mixture models

Version

4.1c

Usage instructions

module load phylobayes/4.1c

Link to user guide/tutorial

http://www.atgc-montpellier.fr/download/binaries/phylobayes/phylobayes3.3.pdf

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Phyml

Software link to site

http://www.atgc-montpellier.fr/phyml/

Description

PhyML estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.

Version

20150402

Usage instructions

module load phyml/20150402

Link to user guide/tutorial

http://www.atgc-montpellier.fr/download/papers/phyml_manual_2012.pdf

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Picard

Software link to site

https://broadinstitute.github.io/picard/

Description

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

Version

1.119, 1.134, 2.1.1, 2.7.1, 2.18.4, 2.18.23

Usage instructions

module load picard/xxx (where xxx represents version number)

Link to user guide/tutorial

https://broadinstitute.github.io/picard/command-line-overview.html

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pigz

Software link to site

https://zlib.net/pigz/

Description

pigz stands for parallel implementation of gzip

Version

2.3.4

Usage instructions

module load pigz

Link to user guide/tutorial

https://zlib.net/pigz/

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Pilon

Software link to site

https://github.com/broadinstitute/pilon/wiki

Description

Pilon is an automated genome assembly improvement and variant detection tool.

Version

1.20, 1.22

Usage instructions

None

Link to user guide/tutorial

https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage

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Pindel

Software link to site

http://gmt.genome.wustl.edu/packages/pindel/background.html

Description

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-base resolution from next-gen sequence data.

Version

20150416

Usage instructions

module load pindel/20150416

Link to user guide/tutorial

http://gmt.genome.wustl.edu/packages/pindel/user-manual.html

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Pipits

Software link to site

https://github.com/hsgweon/pipits

Description

PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.

Version

1.2.0, 2.2

Usage instructions

module load pipits/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/hsgweon/pipits

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Pixman

Software link to site

http://www.pixman.org/

Description

None

Version

0.32.6

Usage instructions

module load pixman/0.32.6

Link to user guide/tutorial

http://www.pixman.org/

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Platypus

Software link to site

http://www.well.ox.ac.uk/platypus

Description

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data

Version

0.8.1

Usage instructions

module load platypus

Link to user guide/tutorial

http://www.well.ox.ac.uk/platypus-doc

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PLINK

Software link to site

http://zzz.bwh.harvard.edu/plink/

Description

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Version

1.07, 1.90, 2.0

Usage instructions

module load plink/xxx (replace xxx with the version you want)

Link to user guide/tutorial

http://zzz.bwh.harvard.edu/plink/dist/plink-doc-1.07.pdf

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Plplot

Software link to site

http://plplot.sourceforge.net/

Description

None

Version

5.11.1

Usage instructions

module load plplot/5.11.1

Link to user guide/tutorial

http://plplot.sourceforge.net/documentation.php

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Plumed

Software link to site

http://www.plumed.org/

Description

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.

Version

2.2.4, 2.3.0

Usage instructions

module load plumed/2.2.4 or module load plumed/2.3.0

Link to user guide/tutorial

http://www.plumed.org/documentation

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PneumoCaT

Software link to site

https://github.com/phe-bioinformatics/PneumoCaT

Description

Pneumococcal Capsular Typing tool for NGS data

Version

1.0

Usage instructions

module load pneumocat

Link to user guide/tutorial

https://github.com/phe-bioinformatics/PneumoCaT

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PneumoCaT

Software link to site

https://github.com/phe-bioinformatics/PneumoCaT

Description

Pneumococcal Capsular Typing tool for NGS data

Version

1.3

Usage instructions

module load pneumocat/1.3

Link to user guide/tutorial

https://github.com/phe-bioinformatics/PneumoCaT

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Poppler

Software link to site

https://poppler.freedesktop.org/

Description

None

Version

0.31.0

Usage instructions

module load poppler/0.31.0

Link to user guide/tutorial

https://freedesktop.org/wiki/Software/poppler/

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Povray

Software link to site

http://www.povray.org/

Description

A tool for creating 3D graphics.

Version

3.6.1

Usage instructions

module load povray/3.6.1

Link to user guide/tutorial

http://wiki.povray.org/content/Documentation:Contents

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pplacer

Software link to site

https://matsen.fhcrc.org/pplacer/

Description

Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

Version

v1.1.alpha19

Usage instructions

module load pplacer

Link to user guide/tutorial

https://matsen.fhcrc.org/pplacer/

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Prank

Software link to site

http://wasabiapp.org/software/prank/

Description

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.

Version

150803

Usage instructions

module load prank/150803

Link to user guide/tutorial

http://wasabiapp.org/software/prank/

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Preseq

Software link to site

http://smithlabresearch.org/software/preseq/

Description

PRESEQ Software for predicting library complexity and genome coverage in high-throughput sequencing.

Version

2.0

Usage instructions

module load preseq

Link to user guide/tutorial

http://smithlabresearch.org/software/preseq/

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Prinseq

Software link to site

http://prinseq.sourceforge.net/

Description

PReprocessing and INformation of SEQuence data.

Version

0.20.4

Usage instructions

module load prinseq/0.20.4

Link to user guide/tutorial

http://prinseq.sourceforge.net/manual.html

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Prodigal

Software link to site

https://github.com/hyattpd/Prodigal

Description

Prodigal Gene Prediction Software.

Version

2.6.3

Usage instructions

module load prodigal/2.6.3

Link to user guide/tutorial

https://github.com/hyattpd/prodigal/wiki

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Proj

Software link to site

http://proj4.org/

Description

PROJ.4 Cartographic Projections library.

Version

4.9.1, 4.9.3

Usage instructions

module load proj/4.9.1 or module load proj/4.9.3

Link to user guide/tutorial

http://proj4.org/

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Proj.4

Software link to site

http://proj4.org/

Description

PROJ.4 Cartographic Projections library.

Version

4.9.3

Usage instructions

module load proj.4/4.9.3

Link to user guide/tutorial

http://proj4.org/

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Prokka

Software link to site

http://www.vicbioinformatics.com/software.prokka.shtml

Description

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

Version

1.11, 1.12, 1.13.3

Usage instructions

module load prokka/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.vicbioinformatics.com/documents/Quick_Start_Guide_BLAST_to_BLAST+.pdf

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ProteinOrtho

Software link to site

https://www.bioinf.uni-leipzig.de/Software/proteinortho

Description

Proteinortho is a tool to detect orthologous genes within different species.

Version

v5.16

Usage instructions

module load proteinortho

Link to user guide/tutorial

https://www.bioinf.uni-leipzig.de/Software/proteinortho/manual.html

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Protobuf

Software link to site

https://developers.google.com/protocol-buffers/

Description

Protocol buffers are a language-neutral, platform-neutral extensible mechanism for serializing structured data.

Version

2.6.1, 3.5.1

Usage instructions

module load protobuf/2.6.1 or module load protobuf/3.5.1

Link to user guide/tutorial

https://developers.google.com/protocol-buffers/docs/overview

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PSIPRED

Software link to site

http://bioinf.cs.ucl.ac.uk/psipred/

Description

The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location.

Version

4.0

Usage instructions

module load psipred

Link to user guide/tutorial

http://bioinf.cs.ucl.ac.uk/psipred/

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Pslib

Software link to site

http://pslib.sourceforge.net/

Description

pslib is a C-library to create PostScript files on the fly.

Version

0.4.5

Usage instructions

module load pslib/0.4.5

Link to user guide/tutorial

https://sourceforge.net/p/pslib/wiki/Home/

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PSMC

Software link to site

https://github.com/lh3/psmc

Description

This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.

Version

0.6.5-r67

Usage instructions

module load psmc/0.6.5-r67

Link to user guide/tutorial

https://github.com/lh3/psmc

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pugixml

Software link to site

https://pugixml.org/

Description

Light-weight, simple and fast XML parser for C++

Version

1.9

Usage instructions

module load pugixml

Link to user guide/tutorial

https://pugixml.org/

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Purge Haplotigs

Software link to site

https://bitbucket.org/mroachawri/purge_haplotigs

Description

Pipeline to help with curating heterozygous diploid genome assemblies

Version

1.0

Usage instructions

module load purge_haplotigs

Link to user guide/tutorial

https://bitbucket.org/mroachawri/purge_haplotigs

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Pymol

Software link to site

https://www.pymol.org/

Description

A user-sponsored molecular visualization system on an open-source foundation.

Version

20150522

Usage instructions

module load pymol/20150522

Link to user guide/tutorial

https://www.pymol.org/

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Python

Software link to site

https://www.python.org/

Description

Python is a programming language that lets you work more quickly and integrate your systems more effectively.

Version

2.7.9, 2.7.10, 2.7.11, 2.7.13, 2,7.15, 2.7.15-intel, 3.4.3, 3.5.1, 3.5.1-b2, 3.6.5, 3.6.5-intel, 3.7.2, 3.7.3, 3.7.3-intel

Usage instructions

module load python/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.python.org/doc/

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Qe

Software link to site

http://www.quantum-espresso.org/

Description

Quantum-Expresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.

Version

6.0, 6.0-impi

Usage instructions

module load qe/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.quantum-espresso.org/users-manual/

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Qhull

Software link to site

http://www.qhull.org/

Description

None

Version

2012.1

Usage instructions

module load qhull/2012.1

Link to user guide/tutorial

http://www.qhull.org/html/index.htm#TOC

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Qiime

Software link to site

http://qiime.org/

Description

QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

Version

py2.7.9, py2.7.10

Usage instructions

module load qiime/py2.7.9, module load qiime/py2.7.10

Link to user guide/tutorial

http://qiime.org/

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Qorts

Software link to site

https://github.com/hartleys/QoRTs

Description

The QoRTs software package is a fast, efficient, and portable multifunction toolkit designed to assist in the analysis, quality control, and data management of RNA-Seq datasets.

Version

1.1.8

Usage instructions

module load qorts/1.1.8

Link to user guide/tutorial

http://hartleys.github.io/QoRTs/index.html

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Qt

Software link to site

https://www.qt.io/

Description

Qt is a flexible and customisable framework.

Version

3.3.8b, 5.4.0, 5.5.1, 5.7.0, 5.8.0

Usage instructions

module load qt/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.qt.io/whitepapers/

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Qualimap

Software link to site

http://qualimap.bioinfo.cipf.es/

Description

Qualimap is a platform-independent application written in Java and R that provides an interface to facilitate the quality control of alignment sequencing data.

Version

2.2.1

Usage instructions

module load qualimap/2.2.1

Link to user guide/tutorial

http://qualimap.bioinfo.cipf.es/doc_html/index.html

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QUAST

Software link to site

http://bioinf.spbau.ru/quast

Description

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.

Version

3.2, 4.3, 5.0.2

Usage instructions

module load quast/xxx (where xxx is the version)

Link to user guide/tutorial

http://quast.bioinf.spbau.ru/manual.html

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QuickTree

Software link to site

https://github.com/tseemann/quicktree

Description

QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.

Version

2.0, 2.4

Usage instructions

module load quicktree/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/tseemann/quicktree

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Qwt

Software link to site

http://qwt.sourceforge.net/

Description

Qwt is a graphics extension to the Qt GUI application framework.

Version

4.2.0

Usage instructions

module load qwt/4.2.0

Link to user guide/tutorial

http://qwt.sourceforge.net/

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R

Software link to site

https://www.r-project.org/

Description

Free software environment for statistical computing and graphics.

Version

3.1.2, 3.2.2, 3.3.0, 3.3.2, 3.4.0, 3.4.4, 3.5.0, 3.5.1, 3.5.2, 3.6.0

Usage instructions

module load R/xxx (where xxx is the version number)

Link to user guide/tutorial

https://cran.r-project.org/manuals.html

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Racon

Software link to site

https://github.com/isovic/racon

Description

Consensus module for raw de novo DNA assembly of long uncorrected reads.

Version

1.3.1

Usage instructions

module load racon/1.3.1

Link to user guide/tutorial

https://github.com/isovic/racon

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Ragout

Software link to site

https://github.com/fenderglass/Ragout

Description

A tool for reference-assisted assembly.

Version

2.0b

Usage instructions

module load ragout/2.0b

Link to user guide/tutorial

https://github.com/fenderglass/Ragout

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RAiSD

Software link to site

https://github.com/alachins/raisd

Description

RAiSD (Raised Accuracy in Sweep Detection) is a stand-alone software implementation of the ? statistic for selective sweep detection.

Version

1.7

Usage instructions

modue load raisd

Link to user guide/tutorial

https://github.com/alachins/raisd

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RapidJSON

Software link to site

http://rapidjson.org/index.html

Description

A fast JSON parser/generator for C++ with both SAX/DOM style API

Version

1.1.0

Usage instructions

module load rapidjson/1.1.0

Link to user guide/tutorial

http://rapidjson.org/index.html

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Raxml

Software link to site

http://sco.h-its.org/exelixis/web/software/raxml/

Description

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).

Version

8.1.17, 8.2

Usage instructions

module load raxml/8.1.17 or module load raxml/8.2

Link to user guide/tutorial

http://sco.h-its.org/exelixis/resource/download/NewManual.pdf

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Raxmls

Software link to site

http://sco.h-its.org/exelixis/web/software/raxml/

Description

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML).

Version

8.1.17

Usage instructions

module load raxmls/8.1.17

Link to user guide/tutorial

http://sco.h-its.org/exelixis/web/software/raxml/#documentation

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Ray

Software link to site

http://denovoassembler.sourceforge.net/

Description

Parallel genome assemblies for parallel DNA sequencing.

Version

2.3.1

Usage instructions

module load ray/2.3.1

Link to user guide/tutorial

http://denovoassembler.sourceforge.net/manual.html

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Rdpclassifier

Software link to site

https://github.com/rdpstaff/classifier

Description

The RDP Classifier is a naive Bayesian classifier that rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.

Version

2.2

Usage instructions

module load rdpclassifier/2.2

Link to user guide/tutorial

https://github.com/rdpstaff/classifier

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Re2

Software link to site

https://github.com/google/re2

Description

RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library.

Version

0.0.0

Usage instructions

module load re2/0.0.0

Link to user guide/tutorial

https://github.com/google/re2/wiki

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Readline

Software link to site

https://tiswww.case.edu/php/chet/readline/rltop.html

Description

GNU readline library.

Version

6.3, 6.3-test

Usage instructions

module load readline/6.3 or module load readline/6.3-test

Link to user guide/tutorial

https://tiswww.case.edu/php/chet/readline/rltop.html#Documentation

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Readosm

Software link to site

https://www.gaia-gis.it/fossil/readosm/index

Description

ReadOSM is an open source library to extract valid data from within an Open Street Map input file.

Version

1.0.0e

Usage instructions

module load readosm/1.0.0e

Link to user guide/tutorial

http://www.gaia-gis.it/gaia-sins/readosm-1.1.0-doxy-doc/index.html

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Readseq

Software link to site

http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

Description

Guesses what your input biosequence data format is, and converts it to what your software knows how to handle.

Version

2.1.30

Usage instructions

module load readseq

Link to user guide/tutorial

http://iubio.bio.indiana.edu/soft/molbio/readseq/java/readseq-help.html

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REAPR

Software link to site

https://www.sanger.ac.uk/science/tools/reapr

Description

REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison.

Version

1.0.18

Usage instructions

module load reapr/1.0.18

Link to user guide/tutorial

https://www.sanger.ac.uk/science/tools/reapr

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Reddog

Software link to site

https://github.com/katholt/RedDog

Description

This program implements a workflow pipeline for short read length sequencing analysis, including the read mapping task, through to variant detection, followed by analyses (SNPs only).

Version

V1beta.8

Usage instructions

module load reddog/V1beta.8

Link to user guide/tutorial

https://github.com/katholt/RedDog/wiki/1.-Instruction-Manual#reddog-v049---instruction-manual

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Repeatmasker

Software link to site

http://www.repeatmasker.org/

Description

A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Version

4.0.6, 4.0.7

Usage instructions

module load repeatmasker/4.0.6 or module load repeatmasker/4.0.7

Link to user guide/tutorial

http://www.repeatmasker.org/faq.html

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Repeatmodeler

Software link to site

http://www.repeatmasker.org/RepeatModeler.html

Description

A de-novo repeat family identification and modeling package.

Version

1.0.8, 1.0.11

Usage instructions

module load repeatmodeler/1.0.8 or repeatmodeler/1.0.11

Link to user guide/tutorial

http://www.repeatmasker.org/faq.html

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RepeatScout

Software link to site

https://bix.ucsd.edu/repeatscout/

Description

RepeatScout is a tool to discover repetitive substrings in DNA.

Version

1.0.5

Usage instructions

module load repeatscout/1.0.5

Link to user guide/tutorial

https://bix.ucsd.edu/repeatscout/readme.1.0.5.txt

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Rgdal

Software link to site

https://cran.r-project.org/web/packages/rgdal/index.html

Description

Free software environment for statistical computing and graphics. Note: This version loads dependencies to allow use of the rgdal (Geospatial Data Abstraction) Library.

Version

3.1.2

Usage instructions

module load rgdal/3.1.2

Link to user guide/tutorial

https://cran.r-project.org/web/packages/rgdal/rgdal.pdf

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Rmats

Software link to site

http://rnaseq-mats.sourceforge.net/rmats3.0.9/

Description

Multivariate Analysis of Transcript Splicing (MATS) is a computational tool to detect differential alternative splicing events from RNA-Seq data.

Version

3.0.9, 3.2.5

Usage instructions

module load rmats/3.0.9 or module load rmats/3.0.9

Link to user guide/tutorial

http://rnaseq-mats.sourceforge.net/rmats3.0.9/user_guide.htm

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Rnammer

Software link to site

http://www.cbs.dtu.dk/services/RNAmmer/

Description

RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

Version

1.2

Usage instructions

module load rnammer/1.2

Link to user guide/tutorial

http://www.cbs.dtu.dk/services/RNAmmer/

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Roary

Software link to site

https://sanger-pathogens.github.io/Roary/

Description

Roary is a high speed stand alone pan genome pipeline.

Version

3.6.1, 3.11.2

Usage instructions

module load roary/3.6.1

Link to user guide/tutorial

https://sanger-pathogens.github.io/Roary/

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RocksDB

Software link to site

https://rocksdb.org/

Description

A library that provides an embeddable, persistent key-value store for fast storage

Version

5.18.3

Usage instructions

module load rocksdb/5.18.3

Link to user guide/tutorial

https://rocksdb.org/docs/

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Root

Software link to site

https://root.cern.ch/

Description

ROOT provides functionalities needed to deal with big data processing, statistical analysis, visualisation and storage.

Version

5.34.34, 6.04.14

Usage instructions

module load root/5.34.34 or module load root/6.04.14

Link to user guide/tutorial

https://root.cern.ch/documentation

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Rosetta

Software link to site

https://www.rosettacommons.org/

Description

Rosetta is a library-based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

Version

2015.19.57819

Usage instructions

module load rosetta/2015.19.57819

Link to user guide/tutorial

https://www.rosettacommons.org/docs/latest/Home

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Routino

Software link to site

http://www.routino.org/

Description

Routino is an application for finding a route between two points using the dataset of topographical information collected byhttp://www.OpenStreetMap.org.

Version

2.7.3

Usage instructions

module load routino/2.7.3

Link to user guide/tutorial

http://www.routino.org/documentation/

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RSEM

Software link to site

http://deweylab.github.io/RSEM/

Description

A software package for estimating gene and isoform expression levels from RNA-Seq data.

Version

1.2.29, 1.3.1

Usage instructions

module load rsem/xxx (where xxx is the version)

Link to user guide/tutorial

http://deweylab.github.io/RSEM/

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Rstudio

Software link to site

https://www.rstudio.com/

Description

An integrated development environment (IDE) for R.

Version

1.0.136

Usage instructions

module load rstudio/1.0.136

Link to user guide/tutorial

https://www.rstudio.com/online-learning/

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rtk

Software link to site

http://www.openrtk.org/

Description

Cross-platform software for fast circular cone-beam CT reconstruction based on the Insight Toolkit (ITK)

Version

1.4.0

Usage instructions

module load rtk

Link to user guide/tutorial

http://www.openrtk.org/Doxygen/index.html

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Ruby

Software link to site

https://www.ruby-lang.org/en/

Description

None

Version

2.2.2, 2.5.1, 2.6.3

Usage instructions

module load ruby/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.ruby-lang.org/en/documentation/

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Salmon

Software link to site

https://github.com/COMBINE-lab/salmon

Description

Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.

Version

0.8.2, 0.11.0, 0.12.0, 0.13.1

Usage instructions

module load salmon/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/COMBINE-lab/salmon

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sam2bam

Software link to site

https://github.com/t-ogasawara/sam-to-bam

Description

sam2bam provides file format conversion from SAM to BAM, as a basic feature.

Version

1.2

Usage instructions

module load sam2bam/1.2

Link to user guide/tutorial

http://t-ogasawara.github.io/sam-to-bam/

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Sambamba

Software link to site

https://github.com/lomereiter/sambamba

Description

Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.

Version

0.6.4

Usage instructions

module load sambamba/0.6.4

Link to user guide/tutorial

https://github.com/lomereiter/sambamba/wiki

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Samblaster

Software link to site

https://github.com/GregoryFaust/samblaster

Description

Samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.

Version

0.1.22

Usage instructions

module load samblaster/0.1.22

Link to user guide/tutorial

https://github.com/GregoryFaust/samblaster

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samclip

Software link to site

https://github.com/tseemann/samclip

Description

Filter SAM file for soft and hard clipped alignments.

Version

0.2

Usage instructions

module load samclip

Link to user guide/tutorial

https://github.com/tseemann/samclip

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Samtools

Software link to site

http://www.htslib.org/

Description

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Version

0.1.18, 0.1.19, 1.1-intel, 1.2, 1.3-intel, 1.3.1, 1.3.1-intel, 1.5, 1.5-intel, 1.6, 1.6-intel, 1.8, 1.9

Usage instructions

module load samtools/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.htslib.org/doc/#manual-pages

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SAS

Software link to site

https://www.sas.com/

Description

SAS (Statistical Analysis System) is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics.

Version

9.4

Usage instructions

module load sas/9.4

Link to user guide/tutorial

http://support.sas.com/documentation/94/

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Scala

Software link to site

https://www.scala-lang.org/

Description

Scala is a general-purpose programming language providing support for functional programming and a strong static type system.

Version

2.11.11

Usage instructions

module loaod scala/2.11.11

Link to user guide/tutorial

http://docs.scala-lang.org/

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ScaLAPACK

Software link to site

http://www.netlib.org/scalapack/

Description

A library of high-performance linear algebra routines for parallel distributed memory machines

Version

1.0

Usage instructions

module load pneumocat

Link to user guide/tutorial

http://netlib.org/scalapack/slug/index.html

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Scons

Software link to site

http://scons.org/

Description

A software construction tool (build tool, or make tool) implemented in Python, that uses Python scripts as configuration files for software builds.

Version

2.3.4

Usage instructions

module load scons/2.3.4

Link to user guide/tutorial

http://scons.org/documentation.html

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Scotch

Software link to site

http://www.labri.fr/perso/pelegrin/scotch/

Description

Programs and libraries for graph, mesh and hypergraph partitioning

Version

6.0.6

Usage instructions

module load scotch/6.0.6

Link to user guide/tutorial

https://gforge.inria.fr/docman/view.php/248/8261/ptscotch_user6.0.pdf

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scotti

Software link to site

https://omictools.com/structured-coalescent-transmission-tree-inference-tool

Description

SCOTTI (Structured COalescent Transmission Tree Inference) is a BEAST 2 package to reconstruct transmission trees from genetic data of the pathogen and epidemiological data simultaneously.

Version

1.1.0

Usage instructions

module load scotti

Link to user guide/tutorial

https://omictools.com/structured-coalescent-transmission-tree-inference-tool

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SDL

Software link to site

https://www.libsdl.org/

Description

Simple DirectMedia Layer is a cross-platform development library

Version

1.2.15, 2.0.9

Usage instructions

module load sdl/xxx (where xxx is the version

Link to user guide/tutorial

http://wiki.libsdl.org/FrontPage

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SDL_image

Software link to site

https://www.libsdl.org/projects/SDL_image/

Description

SDL_image is an image file loading library.

Version

1.2.12

Usage instructions

module load sdl_image/1.2.12

Link to user guide/tutorial

https://www.libsdl.org/projects/SDL_image/docs/index.html

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SecretomeP

Software link to site

http://www.cbs.dtu.dk/services/SecretomeP-1.0/

Description

SecretomeP 1.0 produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion in eukaryotes.

Version

1.0

Usage instructions

module load secretomep

Link to user guide/tutorial

http://www.cbs.dtu.dk/services/SecretomeP-1.0/

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selscan

Software link to site

https://github.com/szpiech/selscan

Description

Calculates EHH-based scans for positive selection in genomes

Version

1.2.0a

Usage instructions

module load selscan/1.2.0a

Link to user guide/tutorial

https://github.com/szpiech/selscan

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SeqKit

Software link to site

https://bioinf.shenwei.me/seqkit/

Description

A cross-platform and ultrafast toolkit for FASTA

Version

1.10.1

Usage instructions

module load seqkit

Link to user guide/tutorial

https://bioinf.shenwei.me/seqkit/

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seqOutBias

Software link to site

https://guertinlab.github.io/seqOutBias/

Description

Universal correction of enzymatic sequence bias.

Version

1.1.3

Usage instructions

module load seqoutbias/1.1.3

Link to user guide/tutorial

https://guertinlab.github.io/seqOutBias/seqOutBias_user_guide.pdf

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Seqtk

Software link to site

https://github.com/lh3/seqtk

Description

Toolkit for processing sequences in FASTA/Q formats

Version

1.0, 1.3

Usage instructions

module load seqtk/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/lh3/seqtk

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sff2fastq

Software link to site

https://github.com/indraniel/sff2fastq

Description

Extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.

Version

0.9.2

Usage instructions

module load sff2fastq/0.9.2

Link to user guide/tutorial

https://github.com/indraniel/sff2fastq

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Sga

Software link to site

https://github.com/jts/sga

Description

A de novo sequence assembler using string graphs.

Version

0.10.14, 0.10.15

Usage instructions

module load sga/0.10.14 or module load sga/0.10.15

Link to user guide/tutorial

https://github.com/jts/sga/wiki

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SHAPEIT

Software link to site

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Description

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

Version

2.12

Usage instructions

module load shapeit/2.12

Link to user guide/tutorial

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gettingstarted

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Shorah

Software link to site

http://cbg-ethz.github.io/shorah/

Description

Short Reads Assembly into Haplotypes.

Version

0.5.1

Usage instructions

module load shorah/0.5.1

Link to user guide/tutorial

http://ozagordi.github.io/shorah/

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ShortStack

Software link to site

https://github.com/MikeAxtell/ShortStack

Description

Alignment of small RNA-seq data and annotation of small RNA-producing genes

Version

3.8.4

Usage instructions

module load shortstack/3.8.4

Link to user guide/tutorial

https://github.com/MikeAxtell/ShortStack

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shovill

Software link to site

https://github.com/tseemann/shovill

Description

Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get near-identical results in far less time.

Version

0.5, 1.0-pre1

Usage instructions

module load shovill/xxx (replace xxx with the version)

Link to user guide/tutorial

https://github.com/tseemann/shovill

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Sibelia

Software link to site

http://bioinf.spbau.ru/sibelia

Description

Genome comparison via de Bruijn graph.

Version

3.0.6

Usage instructions

module load sibelia/3.0.6

Link to user guide/tutorial

http://bioinf.spbau.ru/sibelia/examples

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Siesta

Software link to site

https://departments.icmab.es/leem/siesta/

Description

SIESTA performs efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Version

4.0, 4.1-b1

Usage instructions

module load siesta/xxx (where xxx is the version)

Link to user guide/tutorial

https://departments.icmab.es/leem/siesta/Documentation/Manuals/manuals.html

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Signalp

Software link to site

http://www.cbs.dtu.dk/services/SignalP/

Description

SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.

Version

4.1e, 4.1f

Usage instructions

module load signalp/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.cbs.dtu.dk/services/SignalP/

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SiLiX

Software link to site

http://lbbe.univ-lyon1.fr/SiLiX?lang=en

Description

SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.

Version

1.2.11

Usage instructions

module load silix

Link to user guide/tutorial

http://lbbe.univ-lyon1.fr/Documentation,3012.html?lang=en

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Simple

Software link to site

http://simplecryoem.com/

Description

Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles.

Version

2.1

Usage instructions

module load simple/2.1

Link to user guide/tutorial

http://simplecryoem.com/manuals.html

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Singularity

Software link to site

https://sylabs.io/singularity/

Description

A container application for reproducible research computing

Version

3.2.1

Usage instructions

module load singularity/3.2.1

Link to user guide/tutorial

https://sylabs.io/docs/

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SKESA

Software link to site

https://bioconda.github.io/recipes/skesa/README.html

Description

Strategic Kmer Extension for Scrupulous Assemblies

Version

2.2, 2.3

Usage instructions

module load skesa/xxx (where xxx is the version)

Link to user guide/tutorial

https://bioconda.github.io/recipes/skesa/README.html

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Slang

Software link to site

http://brewformulas.org/s-lang

Description

S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software.

Version

0.9.6, 2.3.0

Usage instructions

module load slang/0.9.6 or module load slang/2.3.0

Link to user guide/tutorial

http://www.jedsoft.org/slang/docs.html

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SLEPc

Software link to site

http://slepc.upv.es/

Description

SLEPc the Scalable Library for Eigenvalue Problem Computations

Version

3.7.4

Usage instructions

module load slepc/3.7.4

Link to user guide/tutorial

http://slepc.upv.es/documentation/

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SLiMSuite

Software link to site

http://www.slimsuite.unsw.edu.au/software.php

Description

Short Linear Motif discovery and analysis

Version

1.8.1

Usage instructions

module load slimsuite/1.8.1

Link to user guide/tutorial

http://www.slimsuite.unsw.edu.au/software.php

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Smalt

Software link to site

http://www.sanger.ac.uk/science/tools/smalt-0

Description

SMALT aligns DNA sequencing reads with genomic reference sequences.

Version

0.7.6

Usage instructions

module load smalt/0.7.6

Link to user guide/tutorial

https://sourceforge.net/projects/smalt/files/smalt_manual.pdf/download

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SMRT

Software link to site

http://www.pacb.com

Description

PacBios open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data (command line only).

Version

2.3.0

Usage instructions

module load smrt/2.3.0

Link to user guide/tutorial

https://www.pacb.com/support/documentation/

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SMRTtools

Software link to site

http://www.pacb.com

Description

PacBio's open-source SMRT Analysis software smrttools only

Version

6.0.0

Usage instructions

module load smrttools/6.0.0

Link to user guide/tutorial

https://www.pacb.com/support/documentation/

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SNAP

Software link to site

http://snap.cs.berkeley.edu/

Description

Scalable Nucleotide Alignment Program

Version

1.0beta.23

Usage instructions

module load snap/1.0beta.23

Link to user guide/tutorial

http://snap.cs.berkeley.edu/downloads/snap-1.0beta-manual.pdf

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Snappy

Software link to site

https://github.com/google/snappy

Description

A fast compressor.

Version

1.1.3

Usage instructions

module load snappy/1.1.3

Link to user guide/tutorial

https://github.com/google/snappy

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Snippy

Software link to site

https://github.com/tseemann/snippy

Description

Snippy finds variants between a haploid reference genome and your NGS sequence reads.

Version

3.1, 3.2, 4.0-dev2, 4.0.5, 4.1.0, 4.3.5

Usage instructions

module load snippy/xxx (replace xxx with the version you want)

Link to user guide/tutorial

https://github.com/tseemann/snippy

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snp-dists

Software link to site

https://github.com/tseemann/snp-dists

Description

Pairwise SNP distance matrix from a FASTA sequence alignment

Version

0.2, 0.6

Usage instructions

module load snp-dists/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/tseemann/snp-dists

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SNP-sites

Software link to site

https://github.com/sanger-pathogens/snp-sites

Description

Finds SNP sites from a multi-FASTA alignment file

Version

2.4.1

Usage instructions

module load snp-sites

Link to user guide/tutorial

https://github.com/sanger-pathogens/snp-sites

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SnpEff

Software link to site

http://snpeff.sourceforge.net/SnpEff.html

Description

SnpEff is a variant annotation and effect prediction tool.

Version

4.3t

Usage instructions

module load snpeff/4.3t

Link to user guide/tutorial

http://snpeff.sourceforge.net/SnpEff_manual.html

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SNPhylo

Software link to site

http://chibba.pgml.uga.edu/snphylo/

Description

A pipeline to generate a phylogenetic tree from huge SNP data.

Version

20140701

Usage instructions

module load snphylo

Link to user guide/tutorial

http://chibba.pgml.uga.edu/snphylo/

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SOAPdenovo2

Software link to site

https://github.com/aquaskyline/SOAPdenovo2

Description

Next generation sequencing reads de novo assembler.

Version

2.04-r241

Usage instructions

module load soapdenovo2

Link to user guide/tutorial

https://github.com/aquaskyline/SOAPdenovo2

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SortMeRNA

Software link to site

https://github.com/biocore/sortmerna

Description

SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.

Version

2.1b, 3.0.3

Usage instructions

module load sortmerna/xxx (where xxx is the version)

Link to user guide/tutorial

http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.99-beta.pdf

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Spades

Software link to site

http://bioinf.spbau.ru/spades

Description

SPAdes- St. Petersburg genome assembler- is intended for both standard isolates and single-cell MDA bacteria assemblies.

Version

3.9.0, 3.11.1, 3.12.0

Usage instructions

module load spades/xxx (replace xxx with the version you want)

Link to user guide/tutorial

http://spades.bioinf.spbau.ru/release3.10.1/manual.html

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Spark

Software link to site

https://spark.apache.org

Description

Apache Spark is a fast and general-purpose cluster computing system.

Version

2.2.0

Usage instructions

module load spark/2.2.0

Link to user guide/tutorial

https://spark.apache.org/docs/latest/

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Sparsehash

Software link to site

https://github.com/sparsehash/sparsehash

Description

The sparsehash package consists of two hashtable implementations: sparse, which is designed to be very space efficient, and dense, which is designed to be very time efficient.

Version

2.0.3

Usage instructions

module load sparsehash/2.0.3

Link to user guide/tutorial

https://github.com/sparsehash/sparsehash

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Spatialite

Software link to site

http://www.gaia-gis.it/gaia-sins/

Description

Spatialite-tools are a collection of open source Command Line Interface (CLI) tools supporting SpatiaLite.

Version

4.3.0

Usage instructions

module load spatialite/4.3.0

Link to user guide/tutorial

http://www.gaia-gis.it/gaia-sins/

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SpeedSeq

Software link to site

https://github.com/hall-lab/speedseq

Description

A flexible framework for rapid genome analysis and interpretation

Version

0.1.2

Usage instructions

module load speedseq/0.1.2

Link to user guide/tutorial

https://github.com/hall-lab/speedseq

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Sphinx

Software link to site

http://www.sphinx-doc.org/en/stable/

Description

Sphinx is a tool to easily write documentation. It is written in Python.

Version

1.4a0

Usage instructions

module load sphinx/1.4a0

Link to user guide/tutorial

http://www.sphinx-doc.org/en/stable/contents.html

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Sqlite

Software link to site

https://www.sqlite.org/

Description

None

Version

3080802, 3260000

Usage instructions

module load sqlite/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.sqlite.org/docs.html

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Sratoolkit

Software link to site

https://github.com/ncbi/sratoolkit

Description

The NCBI SRA Toolkit enables reading ('dumping') of sequencing files from the SRA database and writing ('loading') files into the .sra format.

Version

2.5.1, 2.8.0, 2.8.2-1, 2.9.1-1, 2.9.2

Usage instructions

module load sratoolkit/xxx (where xxx represents version number)

Link to user guide/tutorial

https://github.com/ncbi/sratoolkit

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STACKS

Software link to site

http://catchenlab.life.illinois.edu/stacks/

Description

STACKSStacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.

Version

1.46, 1.18, 2.0b

Usage instructions

module load stacks/xxx (replace xxx with the version you want)

Link to user guide/tutorial

http://catchenlab.life.illinois.edu/stacks/manual/

Special licensing notes

(No web interface or sql)

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Stampy

Software link to site

http://www.well.ox.ac.uk/project-stampy

Description

Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome.

Version

1.0.31

Usage instructions

module load stampy/1.0.31

Link to user guide/tutorial

http://www.well.ox.ac.uk/~gerton/README.txt

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Star

Software link to site

https://github.com/alexdobin/STAR

Description

STAR RNA-seq aligner

Version

2.4.0j, 2.5.2a, 2.6.1b, 2.7.0d, 2.7.0e, 2.7.1a

Usage instructions

module load star/xxx (where xxx is the version)

Link to user guide/tutorial

https://github.com/alexdobin/STAR/tree/master/doc

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Strainseeker

Software link to site

http://bioinfo.ut.ee/strainseeker/

Description

StrainSeeker is a program for detecting bacterial strains from raw sequencing reads.

Version

2016-02-10

Usage instructions

module load strainseeker

Link to user guide/tutorial

http://bioinfo.ut.ee/strainseeker/index.php?r=site/page&view=manual

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Strelka

Software link to site

https://sites.google.com/site/strelkasomaticvariantcaller/home

Description

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

Version

1.0.14, 2.9.9

Usage instructions

module load strelka/xxx (where xxx is the version)

Link to user guide/tutorial

https://sites.google.com/site/strelkasomaticvariantcaller/home/faq

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Stringtie

Software link to site

https://ccb.jhu.edu/software/stringtie/

Description

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Version

1.0.4, 1.3.0, 1.3.3b

Usage instructions

module load stringtie/xxx (where xxx is the version number)

Link to user guide/tutorial

https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

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Stxxl

Software link to site

http://stxxl.org/

Description

Standard Template Library for Extra Large Data Sets.

Version

1.4.1

Usage instructions

module load stxxl/1.4.1

Link to user guide/tutorial

http://stxxl.org/tags/master/

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subread

Software link to site

http://subread.sourceforge.net/

Description

Subread package: high-performance read alignment, quantification and mutation discovery

Version

1.5.1

Usage instructions

module load subread

Link to user guide/tutorial

http://subread.sourceforge.net/

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Subread

Software link to site

http://subread.sourceforge.net/

Description

High-performance read alignment, quantification and mutation discovery.

Version

1.5.1

Usage instructions

module load subread/1.5.1

Link to user guide/tutorial

http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

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Subversion

Software link to site

https://subversion.apache.org/

Description

An open source version control system.

Version

1.9.4

Usage instructions

module load subversion/1.9.4

Link to user guide/tutorial

https://subversion.apache.org/docs/

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Suitesparse

Software link to site

http://faculty.cse.tamu.edu/davis/suitesparse.html

Description

SuiteSparse is a suite of sparse matrix algorithms

Version

4.4.3, 4.5.5, 4.5.6

Usage instructions

module load suitesparse/xxx (replace xxx with the version you want)

Link to user guide/tutorial

http://faculty.cse.tamu.edu/davis/suitesparse.html

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SUNDIALS

Software link to site

https://computation.llnl.gov/projects/sundials

Description

Provides robust time integrators and nonlinear solvers that can easily be incorporated into existing simulation codes.

Version

3.1.2, 4.0.1

Usage instructions

module load sundials/xxx (where xxx is the version)

Link to user guide/tutorial

https://computation.llnl.gov/projects/sundials/usage-notes

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Supernova

Software link to site

https://support.10xgenomics.com/de-novo-assembly/software/overview/welcome

Description

Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.

Version

1.1.5, 2.1.1

Usage instructions

module load supernova/xxx (where xxx is the version)

Link to user guide/tutorial

https://support.10xgenomics.com/de-novo-assembly/software/overview/welcome

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Surpi

Software link to site

http://chiulab.ucsf.edu/surpi/

Description

A computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Version

1.0.18

Usage instructions

module load surpi/1.0.18

Link to user guide/tutorial

http://chiulab.ucsf.edu/surpi/

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Svtyper

Software link to site

https://github.com/hall-lab/svtyper

Description

Bayesian genotyper for structural variants.

Version

0.0.2

Usage instructions

module load svtyper/0.0.2

Link to user guide/tutorial

https://github.com/hall-lab/svtyper/blob/master/README.md

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sweed

Software link to site

https://github.com/alachins/sweed

Description

Likelihood-based Selective Sweep Detection

Version

3.2.4

Usage instructions

module load sweed/3.2.4

Link to user guide/tutorial

https://github.com/alachins/sweed

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SweepFinder2

Software link to site

http://www.personal.psu.edu/mxd60/sf2.html

Description

A program written in C that can perform genomic scans for recent selective sweeps selection while controlling for background selection and mutation rate variation.

Version

1

Usage instructions

module load sweepfinder2/1

Link to user guide/tutorial

http://www.personal.psu.edu/mxd60/sf2.html

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Swig

Software link to site

http://www.swig.org/

Description

None

Version

3.0.5

Usage instructions

module load swig/3.0.5

Link to user guide/tutorial

http://www.swig.org/Doc1.1/HTML/Contents.html

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SynerClust

Software link to site

https://github.com/SynerClust/SynerClust

Description

A synteny-aware orthologue clusering tool

Version

1.1

Usage instructions

module load synerclust/1.1

Link to user guide/tutorial

https://github.com/SynerClust/SynerClust

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Tabix

Software link to site

http://www.htslib.org/doc/tabix.html

Description

Tabix indexes a TAB-delimited genome position file and creates an index file.

Version

0.2.6

Usage instructions

module load tabix/0.2.6

Link to user guide/tutorial

http://www.htslib.org/doc/#manual-pages

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tantan

Software link to site

http://cbrc3.cbrc.jp/~martin/tantan/

Description

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.

Version

22

Usage instructions

module load tantan

Link to user guide/tutorial

http://cbrc3.cbrc.jp/~martin/tantan/README.html

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taxator-tk

Software link to site

https://github.com/fungs/taxator-tk

Description

A set of programs for the taxonomic analysis of nucleotide sequence data

Version

1.3.3

Usage instructions

module load taxator-tk

Link to user guide/tutorial

https://github.com/fungs/taxator-tk

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Tbb

Software link to site

https://www.threadingbuildingblocks.org/intel-tbb-tutorial

Description

Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.

Version

4.4

Usage instructions

module load tbb/4.4

Link to user guide/tutorial

https://www.threadingbuildingblocks.org/intel-tbb-tutorial

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Tbl2Asn

Software link to site

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/tbl2asn.txt

Description

A program that automates the submission of sequence records to GenBank.

Version

1.0, 25.6

Usage instructions

module load tbl2asn/xxx (where xxx is the version)

Link to user guide/tutorial

https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/doc/tbl2asn.txt

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Tcl

Software link to site

https://tcl.tk/

Description

Tool command language; a scripting language commonly used for rapid prototyping, scripted applications, GUIs and testing.

Version

8.6.3

Usage instructions

module load tcl/8.6.3

Link to user guide/tutorial

https://tcl.tk/doc/

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TensorFlow

Software link to site

https://www.tensorflow.org/

Description

TensorFlow is designed to facilitate research in machine learning, and to make it quick and easy to transition from research prototype to production system.

Version

refer to /usr/local/tensorflow/README and /usr/local/tensorflow/v100/README on Artemis

Usage instructions

https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/229114058/TensorFlow

Link to user guide/tutorial

https://www.tensorflow.org/community/documentation

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Tk

Software link to site

https://tcl.tk/

Description

Library of basic elements ('widgits') for building a graphical user interface. It is typically used with Tcl.

Version

8.6.3

Usage instructions

module load tk/8.6.3

Link to user guide/tutorial

https://tcl.tk/doc/

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tmux

Software link to site

https://github.com/tmux/tmux/wiki

Description

tmux is a terminal multiplexer.

Version

2.7

Usage instructions

module load tmux/2.7

Link to user guide/tutorial

http://man.openbsd.org/OpenBSD-current/man1/tmux.1

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Tomographer

Software link to site

https://tomographer.github.io/tomographer/

Description

Practical, Reliable Error Bars in Quantum Tomography.

Version

5.4

Usage instructions

module load tomographer

Link to user guide/tutorial

https://tomographer.github.io/tomographer/get-started/

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Tophat

Software link to site

https://ccb.jhu.edu/software/tophat/index.shtml

Description

A spliced read mapper for RNA-Seq.

Version

2.1.0, 2.1.0test

Usage instructions

module load tophat/2.1.0 or module load tophat/2.1.0

Link to user guide/tutorial

https://ccb.jhu.edu/software/tophat/manual.shtml

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Torch

Software link to site

http://torch.ch/

Description

A scientific computing framework with wide support for machine learning algorithms.

Version

7

Usage instructions

module load torch/7

Link to user guide/tutorial

http://torch.ch/docs/getting-started.html#_

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Tracer

Software link to site

http://tree.bio.ed.ac.uk/software/tracer/

Description

Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.

Version

;

Usage instructions

module load tracer/1.6

Link to user guide/tutorial

http://tree.bio.ed.ac.uk/software/tracer/

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Transdecoder

Software link to site

https://transdecoder.github.io/

Description

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Version

2.0.1, 5.5.0

Usage instructions

module load transdecoder/xxx (where xxx is the version)

Link to user guide/tutorial

https://ccb.jhu.edu/software/tophat/manual.shtml

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tre

Software link to site

https://github.com/laurikari/tre

Description

The approximate regex matching library and agrep command line tool.

Version

0.8.0

Usage instructions

module load tre

Link to user guide/tutorial

https://github.com/laurikari/tre

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Trim Galore

Software link to site

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Description

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.

Version

030816, 0.6.1

Usage instructions

module load trimgalore/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.bioinformatics.babraham.ac.uk/training.html

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trimAl

Software link to site

https://github.com/scapella/trimal

Description

A tool for automated alignment trimming in large-scale phylogenetic analyses.

Version

1.4.1

Usage instructions

module load trimal

Link to user guide/tutorial

http://trimal.cgenomics.org/

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Trimmomatic

Software link to site

http://www.usadellab.org/cms/?page=trimmomatic

Description

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

Version

0.33, 0.36, 0.38

Usage instructions

module load trimmomatic/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf

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Trinity

Software link to site

https://github.com/trinityrnaseq/trinityrnaseq

Description

None

Version

2.0.4, 2.1.1, 2.5.1, 2.6.6, 2.8.3

Usage instructions

module load trinity/xxx (where xxx represents version number)

Link to user guide/tutorial

https://github.com/trinityrnaseq/trinityrnaseq/wiki

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Trinotate

Software link to site

https://trinotate.github.io/

Description

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.

Version

3.0.0, 3.1.1

Usage instructions

module load trinotate/xxx (where xxx is the version)

Link to user guide/tutorial

https://trinotate.github.io/

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tRNAscan-SE

Software link to site

http://eddylab.org/software/tRNAscan-SE/

Description

tRNAscan-SE: An improved tool for transfer RNA detection.

Version

1.3.1

Usage instructions

module load tRNAscan/1.3.1

Link to user guide/tutorial

http://eddylab.org/software/tRNAscan-SE/tRNAscan-SE.README

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UCSC Genome Browser

Software link to site

https://genome.ucsc.edu/

Description

UCSC genome browser 'kent' bioinformatic utilities

Version

384

Usage instructions

module load ucsc-userapps

Link to user guide/tutorial

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html

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Udunits

Software link to site

http://www.unidata.ucar.edu/software/udunits/

Description

A C-based package for the programatic handling of units of physical quantities.

Version

2.2.20

Usage instructions

module load udunits/2.2.20

Link to user guide/tutorial

http://www.unidata.ucar.edu/software/udunits/#documentation

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Underworld 2

Software link to site

https://github.com/underworldcode/underworld2

Description

underworld2: A parallel, particle-in-cell, finite element code for Geodynamics.

Version

2

Usage instructions

module load underworld2/2

Link to user guide/tutorial

https://github.com/underworldcode/underworld2

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Usearch

Software link to site

http://www.drive5.com/usearch/

Description

USEARCH is a unique sequence analysis tool.

Version

5.2.236, 6.1, 8.0, 10.0, 11.0.667

Usage instructions

module load usearch/xxx (where xxx represents version number)

Link to user guide/tutorial

http://www.drive5.com/usearch/manual/

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UVP

Software link to site

https://github.com/CPTR-ReSeqTB/UVP

Description

Mycobacterium tuberculosis next generation sequence analysis

Version

2.5.1

Usage instructions

module load uvp/2.5.1

Link to user guide/tutorial

https://github.com/CPTR-ReSeqTB/UVP

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Valgrind

Software link to site

http://valgrind.org/

Description

Valgrind includes six production-quality tools: a memory error detector, two thread error detectors, a cache and branch-prediction profiler, a call-graph generating cache and branch-prediction profiler, and a heap profiler.

Version

3.10.1

Usage instructions

module load valgrind/3.10.1

Link to user guide/tutorial

http://valgrind.org/docs/manual/index.html

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VAPOR

Software link to site

https://www.vapor.ucar.edu/

Description

VAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers.

Version

2.6.0

Usage instructions

module load vapor

Link to user guide/tutorial

https://www.vapor.ucar.edu/docs/usage

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Varscan

Software link to site

http://varscan.sourceforge.net/

Description

Variant detection in massively parallel sequencing.

Version

2.3.9

Usage instructions

module load varscan/2.3.9

Link to user guide/tutorial

http://varscan.sourceforge.net/using-varscan.html

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VaST

Software link to site

https://github.com/FofanovLab/VaST

Description

Variant Site Strain Typer: Identifies the minimum number of variable genomic site that are required to resolve a group of related bacterial strains

Version

1.0

Usage instructions

module load vast

Link to user guide/tutorial

https://github.com/FofanovLab/VaST

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vcf2diploid

Software link to site

https://github.com/abyzovlab/vcf2diploid

Description

Vcf2diploid constructs a personal genome integrating the the variants from the parents and child to the reference genome.

Version

0.2.6a

Usage instructions

module load vcf2diploid

Link to user guide/tutorial

http://info.gersteinlab.org/AlleleSeq

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Vcflib

Software link to site

https://github.com/vcflib/vcflib

Description

A simple C++ library for parsing and manipulating VCF files, + many command-line utilities

Version

1.0.0

Usage instructions

module load vcflib

Link to user guide/tutorial

https://github.com/vcflib/vcflib

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Vcftools

Software link to site

https://vcftools.github.io/index.html

Description

A set of tools written in Perl and C++ for working with VCF files.

Version

0.1.14

Usage instructions

module load vcftools/0.1.14

Link to user guide/tutorial

https://vcftools.github.io/examples.html

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Velvet

Software link to site

https://www.ebi.ac.uk/~zerbino/velvet/

Description

Sequence assembler for very short reads.

Version

1.2.10

Usage instructions

module load velvet/1.2.10

Link to user guide/tutorial

https://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf

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VelvetOptimiser

Software link to site

https://github.com/tseemann/VelvetOptimiser

Description

Automatically optimise three of Velvet's assembly parameters.

Version

2.2.6

Usage instructions

module load velvetoptimiser/2.2.6

Link to user guide/tutorial

https://github.com/tseemann/VelvetOptimiser

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ViennaRNA

Software link to site

https://www.tbi.univie.ac.at/RNA/

Description

The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Version

2.4.2

Usage instructions

module load viennarna/2.4.2

Link to user guide/tutorial

https://www.tbi.univie.ac.at/RNA/documentation.html

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Virtualpg

Software link to site

https://www.gaia-gis.it/fossil/virtualpg/index

Description

VirtualPG is a loadable dynamic extension to both SQLite and SpatiaLite. Its intended scope is supporting direct SQL access to PostgreSQL and PostGIS tables.

Version

1.0.1

Usage instructions

module load virtualpg/1.0.1

Link to user guide/tutorial

https://www.gaia-gis.it/fossil/virtualpg/wiki?name=tutorial

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Visit

Software link to site

https://wci.llnl.gov/codes/visit/

Description

VisIt is a visualization, animation and analysis tool.

Version

2.10.2

Usage instructions

module load visit/2.10.2

Link to user guide/tutorial

https://wci.llnl.gov/simulation/computer-codes/visit/manuals

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Vmatch

Software link to site

http://www.vmatch.de/

Description

A versatile software tool for e?ciently solving large scale sequence matching tasks.

Version

2.3.0

Usage instructions

module load vmatch/2.3.0

Link to user guide/tutorial

http://www.vmatch.de/virtman.pdf

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Vmd

Software link to site

http://www.ks.uiuc.edu/Research/vmd/

Description

Molecular modelling and visualisation program.

Version

1.9.1, 1.9.3

Usage instructions

module load vmd/1.9.1 or module load vmd/1.9.3

Link to user guide/tutorial

http://www.ks.uiuc.edu/Research/vmd/current/docs.html

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Vsearch

Software link to site

https://github.com/torognes/vsearch

Description

VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.

Version

1.8.0, 2.4.3, 2.5.0

Usage instructions

module load vsearch/xxx (where xxx is the version number)

Link to user guide/tutorial

https://github.com/torognes/vsearch/wiki

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Vtk

Software link to site

http://www.vtk.org/

Description

The Visualization Toolkit is an open-source, freely available software system for 3D computer graphics, image processing, and visualization.

Version

5.0.0, 7.1.1

Usage instructions

module load vtk/5.0.0 or module load vtk/7.1.1

Link to user guide/tutorial

http://www.vtk.org/vtk-users-guide/

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WALT

Software link to site

https://github.com/smithlabcode/walt

Description

WALT (Wildcard ALignment Tool) is a read mapping program for bisulfite sequencing in DNA methylation studies.

Version

1.0

Usage instructions

module load walt

Link to user guide/tutorial

https://github.com/smithlabcode/walt

Special licensing notes

GPLv3

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wcslib

Software link to site

http://www.atnf.csiro.au/people/mcalabre/WCS/

Description

WCSLIB 5.16 - an implementation of the FITS WCS standard.

Version

5.16

Usage instructions

module load wcslib

Link to user guide/tutorial

http://www.atnf.csiro.au/people/mcalabre/WCS/

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Wgs

Software link to site

http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page

Description

Whole Genome Shotgun Assembler.

Version

8.3rc2

Usage instructions

module load wgs/8.3rc2

Link to user guide/tutorial

http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page

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wgsim

Software link to site

https://github.com/lh3/wgsim

Description

A small tool for simulating sequence reads from a reference genome.

Version

0.3.1-r13

Usage instructions

module load wgsim

Link to user guide/tutorial

https://github.com/lh3/wgsim

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XCrySDen

Software link to site

http://www.xcrysden.org/

Description

A crystalline and molecular structure visualisation program

Version

1.5.53

Usage instructions

module load xcrysden

Link to user guide/tutorial

http://www.xcrysden.org/Documentation.html

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Xdrfile

Software link to site

https://docs.oracle.com/cd/E23824_01/html/821-1671/xdrnts-1.html

Description

This library allows to read GROMACS trr and xtc files and also to convert from one format to another.

Version

1.1.4

Usage instructions

module load xdrfile/1.1.4

Link to user guide/tutorial

https://docs.oracle.com/cd/E23824_01/html/821-1671/xdrnts-1.html

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XHMM

Software link to site

https://atgu.mgh.harvard.edu/xhmm/index.shtml

Description

The XHMM suite was written to call (CNV) from next-generation sequencing projects, where exome capture was used.

Version

cc14e52

Usage instructions

module load xhmm

Link to user guide/tutorial

https://atgu.mgh.harvard.edu/xhmm/tutorial.shtml

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Xmlto

Software link to site

https://fedorahosted.org/xmlto/

Description

None

Version

0.0.26

Usage instructions

module load xmlto/0.0.26

Link to user guide/tutorial

https://fedorahosted.org/xmlto/wiki/TracGuide

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XP-EHH

Software link to site

https://github.com/joepickrell/xpehh

Description

This is an implementation of XP-EHH, initially described in Sabeti et al. (2007) Genome-wide detection and characterization of positive selection in human populations (

http://www.nature.com/nature/journal/v449/n7164/full/nature06250.html

).

Version

1

Usage instructions

module load xpehh/1

Link to user guide/tutorial

https://github.com/joepickrell/xpehh

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Xz

Software link to site

http://tukaani.org/xz/

Description

XZ Utils is free general-purpose data compression software with a high compression ratio.

Version

5.2.2

Usage instructions

module load xz/5.2.2

Link to user guide/tutorial

https://sourceforge.net/p/lzmautils/discussion/708858

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Yade

Software link to site

https://github.com/yade

Description

Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method.

Version

2018-06-01

Usage instructions

module load yade

Link to user guide/tutorial

https://yade-dem.org/doc/

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yaml-cpp

Software link to site

https://github.com/jbeder/yaml-cpp

Description

yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec.

Version

0.6.2

Usage instructions

module load yaml-cpp/0.6.2

Link to user guide/tutorial

https://github.com/jbeder/yaml-cpp/wiki/Tutorial

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Yasm

Software link to site

http://yasm.tortall.net/

Description

None

Version

1.2.0

Usage instructions

module load yasm/1.2.0

Link to user guide/tutorial

http://yasm.tortall.net/Guide.html

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Zeromq

Software link to site

http://zeromq.org/

Description

ZeroMQ - distributed messaging

Version

4.1.3

Usage instructions

module load zeromq/4.1.3

Link to user guide/tutorial

http://zeromq.org/intro:read-the-manual

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Zlib

Software link to site

http://www.zlib.net/

Description

None

Version

1.2.8, 1.2.11

Usage instructions

module load zlib/xxx (where xxx is the version)

Link to user guide/tutorial

http://www.zlib.net/

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Zstd

Software link to site

https://facebook.github.io/zstd/

Description

Zstandard is a real-time compression algorithm, providing high compression ratios.

Version

1.1.3

Usage instructions

module load zstd/1.1.3

Link to user guide/tutorial

http://facebook.github.io/zstd/zstd_manual.html

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