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

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

Abricate, Abyss, Abyss-mpi, AdapterRemoval, AfterQC, Aligngraph, AlleleSeq, Allpathslg, AmrPlusPlus, 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, Canu, Cap3, CCMetagen, Cd-Hit, Centrifuge, Chimera, Chimeraslayer, ChunkChromosome, Clonalframeml, Clustal Omega, Clustal W/X, CNVnator, Codonphyml, coevol, Cortex, Crest, Cufflinks, Cutadapt, Delly, DETONATE, Diamond, Drive5, 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, 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, Kmc, KohGPI, Kraken, Kraken2, KronaTools, LAST, 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, OrthoFiller, OrthoFinder, Paml, pandaseq, Pblat, Pear, PennCNV, pgdspider, phase, Pheniqs, Phobius, PHYLIP, PhyloBayes, Phyml, Picard, Pilon, Pindel, Pipits, Platypus, PLINK, 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, seqOutBias, Seqtk, sff2fastq, Sga, SHAPEIT, Shorah, ShortStack, shovill, Sibelia, Signalp, SiLiX, SKESA, 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, Tabix, 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

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

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

Anaconda, Anaconda2, Argtable2, Bazel, Binutils, Bison, Cmake, Dbus, Dbus-Glib, Doxygen, 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

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

Ant, GadgetViewer, Geant4, Tomographer, wcslib

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

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

Cairo, cairomm, Circos, Ffmpeg, FreeGLUT, Freetype, Ghostscript, Gnuplot, Graphicsmagick, Idl, 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

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

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

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

Ec2-Api-Tools

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

emacs

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

gcc, Intel, Java, NASM, Pgi

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

Gdb, Re2, Valgrind

gengetopt, Zstd

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

MongoDB, MySQL, Pgsql, RocksDB, Sqlite

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

1.0.0-rc3

module load caffe-3d

ABAQUS Finite Element Analysis products.

6.14-1, 2016

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

Mass screening of contigs for antibiotic resistance genes.

0.3, 0.5, 0.7, 0.8

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

De novo genome sequence assembler.

1.9.0

module load abyss/1.9.0

De novo genome sequence assembler.

1.9.0, 2.0.2

module load abyss-mpi/1.9.0

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.

2.2.2

module load adapterremoval/2.2.2

AFNI (Analysis of Functional NeuroImages)

17.2.02

module load afni

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

0.9.6

module load afterqc/0.9.6

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

2.1.0

module load ag/2.1.0

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

3242011

module load aligngraph/3242011

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

1.2a

module load alleleseq/1.2a

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

52488

module load allpathslg/52488

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.

3.1.0

module load amos/3.1.0

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

0.0.0

module load amrplusplus

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

4.2.0

module load anaconda/4.2.0

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

5.0.1

module load anaconda2/5.0.1

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.

1.1.2

module load ann/1.1.2

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).

20150619, 20170716, 20180416

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

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

180, 181, 182, 190, 191, 192, 193, 2019R1

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

A unified platform for electromagnetic, circuit and system simulation.

170, 181, 182, 193

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

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

1.9.4, 1.10.3

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

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

2.2.0

module load ants

tRNA (and tmRNA) detection.

1.2.36

module load aragorn/1.2.36

An ANSI C library for parsing GNU style command line arguments

13

module load argtable2

A fast download utility.

1.25.0

module load aria2/1.25.0

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

8.500.0

module load armadillo/8.500.0

Multiresolution domain calling software for chromosome conformation capture interaction matricies.

2.2

module load armatus

None

3.1.5

module load arpack-ng/3.1.5

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.

17

module load artemis

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

19_05_2015

module load artfastgen

Automatic Segmentation of Hippocampal Subfields (ASHS)

20170223

module load ashs

Automatically Tuned Linear Algebra Software.

3.10.2, 3.10.3

module load atlas/3.10.2 or module load atlas 3.10.3

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.

3.2.1, 3.3

module load augustus/3.2.1 or module load augustus/3.3

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

2.69

module load autoconf/2.69

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

1.14, 1.15

module load automake/1.14 or module load automake/1.15

count DNA sequence reads in BAM files

0.8.0

module load bam-readcount

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

0.0.50

module load bambamc/0.0.50

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

2.4.0

module load bamtools/2.4.0

Programs for working on SAM/BAM files.

1.0.14

module load bamutil/1.0.14

Bayesian Analysis of Population Structure.

6

module load baps/6

Barrnap predicts the location of ribosomal RNA genes in genomes.

0.6

module load barrnap

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

1.0

module load base/1.0

BaseSpace Sequence Hub Command Line Interface.

0.8.1, 0.9.11.631

module load basespace/0.8.1 or module load basespace/0.9.11.631

Improved mapper for bisulfite sequencing reads on DNA methylation

1.04b

module load batmeth/1.04b

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

3.0.4

module load bayesass

Bazel is a tool that automates software builds and tests.

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

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

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

36.92, 37.98

module load bbmap/36.92 or module load bbmap/37.98

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

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

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

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

2.19

module load bcl2fastq2

Required for supernova

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

20150401

module load beagle/20150401

Bayesian Evolutionary Analysis by Sampling Trees.

1.8.2, 2.2.0, 2.3.1, 2.4.2

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

BEDOPS high-performance genomic feature operations

2.4.30

module load bedops/2.4.30

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

2.24.0, 2.25.0, 2.26.0

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

GNU Binary file utilities.

2.26, 2.30

module load binutils/2.26 or module load binutils/2.30

Tools for early stage alignment file processing

2.0.72

module load biobambam2

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.

2.5

module load biogeme/2.26

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

1

module load biopieces/1

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

0.18.2, 0.19.0, 0.20.0, 0.22.1

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

None

3

module load bison/3

None

3.5.0

module load blas/3.5.0

The PacBio long read aligner

1.3.1

module load blasr/1.3.1

NCBI Basic Local Alignment Search Tool for DNA sequences.

2.2.26, 2.2.30

module load blast/2.2.26 or module load blast/2.2.30

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

2.3.0, 2.4.0, 2.6.0, 2.7.1

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

Web tools to help understand the human genome.

3.6

module load blat/3.6

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

1.0

module load blobtools

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.

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

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

Bowtieis an ultrafast, memory-efficient short read aligner.

1.1.1, 1.1.2

module load bowtie/1.1.1 or module load bowtie/1.1.2

Bowtieis an ultrafast, memory-efficient short read aligner.

2.2.5, 2.3.3.1

module load bowtie2/2.2.5 or module load bowtie2/2.3.3.1

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

3.3a

module load bpp/3.3a

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.

1.0.0

module load bracken/1.0.0

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

1.9

module load braker1

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

2, 2.0.6

module load braker2/2.0 or module load braker2/2.0.6

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

0.95

module load brig/0.95

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.

1.1b, 2.0, 3.0, 3.0.2

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

Bam and Variant Analysis Tools.

1.6

module load bvatools/1.6

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

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

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

None

1.0.6

module load bzip2/1.0.6

Convert3D Medical Image Processing Tool

1.0.0

module load c3d

Caffe is a deep learning framework.

1.0.0-rc3, 1.0.0

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

A New Lightweight, Modular, and Scalable Deep Learning Framework

0.8.1

module load caffe2

None

1.12.18, 1.14.10

module load cairo/1.12.18 or module load cairo/1.14.10

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

1.15.3

module load cairomm

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

a844005b39c2fc7fd5d33c6af977e44248de42cd

module load camino

A single molecule sequence assembler for genomes large and small.

1.3, 1.6, 1.7

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

CAP3 Sequence Assembly Program.

20150421

module load cap3/20150421

None

3.5.0

module load cblas/3.5.0

Microbiome classification pipeline

0.1

module load ccmetagen

A program for clustering and comparing protein or nucleotide sequences.

4.6.1, 4.6.5

module load cd-hit/4.6.1

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

094h

module load cddlib

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

1.0.3-beta, 1.0.4-beta

module load centrifuge/1.0.3-beta

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

3.4.10, 3.41

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

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

4.5.1, 4.7, 4.9, 4.10, 4.11

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

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.

3.2.1

module load cgns/3.2.1

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

1.11

module load chimera/1.11

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

20110519

module load chimeraslayer/20110519

ChunkChromosome is a helper utility for minimac and MaCH.

27-05-14

module load chunkchromosome

Flexible and automatable circular data visualisation.

0.69-3

module load circos/0.69-3

A Class Library for High Energy Physics.

2.1.1.0, 2.2.0.8, 2.3.1.1

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

Efficient inference of recombination in bacterial genomes.

1

module load clonalframeml/1

Multiple alignment of nucleic acid and protein sequences

1.2.4

module load clustal-omega

Multiple alignment of nucleic acid and protein sequences

2.1

module load clustal

Cross-platform, open-source build system.

3.0.1, 3.4.0, 3.9.4, 3.11.4, 3.13.4

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

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

0.4

module load cnvnator

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction.

dev_1.00_201407.24, 20150402

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

Correlated evolution of substitution rates and quantitative traits

1.5

module load coevol/1.5

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

15g, 17a

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

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

1.0.5.21

module load cortex/1.0.5.21

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

0.01

module load crest/0.01

CUDA is NVIDIA's parallel computing architecture.

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

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

CUDA is NVIDIA's parallel computing architecture.

6.0.37, 6.5.14-test,6.5.14, 7.5.18

module load cuda2/6.0.37

Transcriptome assembly and differential expression analysis for RNA-Seq.

2.2.1

module load cufflinks/2.2.1

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

7.59.0

module load curl/7.59.0

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

1.8.3

module load cutadapt/1.8.3

Cyberduck CLI program "duck"

0.6.2

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.

None

1.8.16

module load dbus/1.8.16

None

0.104

module load dbus-glib/0.104

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

1.0.20170624

module load dcm2niix

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

3.6.1

module load dcmtk/3.6.1

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.

0.6.7, 0.7.6, 0.7.8, 0.7.9

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

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

1.11

module load detonate/1.11

Accelerated BLAST compatible local sequence aligner.

0.8.28.90, 0.9.10

module load diamond/0.8.28.90

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

4.07

module load dlpoly/4.07

A documentation system for various programming languages.

1.8.6, 1.8.9.1

module load doxygen/1.8.6 or module load doxygen/1.8.9.1

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

0

module load drive5/0

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

2.3.1

module load dtitk/2.3.1

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

1.1.2-537

module load ea-utils/1.1.2-537

Amazon Elastic Compute Cloud tools.

1.7.5.1

module load ec2-api-tools/1.7.5.1

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.

20150625, 8.60

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

Fungal effector prediction in secretomes

2.0

module load effectorp

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

3.2.4, 3.2.8

module load eigen/3.2.4 or module load eigen/3.2.8

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

2016.05.001, 2018.05.001

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

An extensible and customisable text editor

7.59.0

module load curl/7.59.0

EMBOSS: The European Molecular Biology Open Software Suite.

6.6.0

module load emboss/6.6.0

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

20120210

module load emmax/20120210

Massively parallel phylogenetic placement of genetic sequences

0.2.1-beta

module load epa-ng

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.

3.3.2

module load epacts/3.3.2

None

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

module load epimine/xxx (where xxx represents

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

v1.1.1

module load evidencemodeler

Exabayes is a software package for Bayesian tree inference.

1.5

module load exabayes/1.5

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

1.1.2

module load excavator2tool/1.1.2

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

1

module load exciting

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.

2.2.0_x86_64

module load exonerate

GPL

None

2.1.0

module load expat/2.1.0

FALCON: experimental PacBio diploid assembler

0.1, 0.5

module load falcon/0.1 or module load falcon/0.5

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

52016

module load falcon-unzip/52016

Comprehensive, accurate and fast distance-based phylogeny inference program

2.1.5

module load fastme

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

3.1, 3.1-b

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

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

0.19.6

module load fastp/0.19.6

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

1.4.8

module load fastphase

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

0.11.3, 0.11.7

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

The fastQValidator validates the format of fastq files.

0.1.1a

module load fastqvalidator/0.1.1a

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

2.1.8, 2.1.9, 2.1.10

module load fasttree/2.1.8 or module load fasttree/2.1.9

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

0.0.14

module load fastx/0.0.14

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

2018.2.0.dev0

module load fenics/2018.2.0.dev0

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.

2.8, 3.4.2

module load ffmpeg/2.8 or module load ffmpeg/3.4.2

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

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

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

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

0.9.0-snapshot

module load fgbio

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

2.2

module load fimpute/2.2

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

1.06

module load fix/1.06

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.

1.2.11

module load flash/1.2.11

None

2.5.39

module load flex/2.5.39

None

2.11.92

module load fontconfig/2.11.92

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

0.4.4

module load fqgrep

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

2.1

module load fqtools/2.1

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.

1.31

module load fraggenescan

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

2.0.0

module load franz

Bayesian haplotype-based polymorphism discovery and genotyping.

1.0.2-33, 1.2.0

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

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

2.6.0, 3.0.0

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

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

dev, 5.3.0, 6

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

None

2.5.5

module load freetype/2.5.5

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

1.0.2

module load freexl/1.0.2

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

5.0.8, 5.0.9, 6.0.1

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

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

0.7.2, 1.2

module load funannotate/0.72 or module load funannotate/1.2

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

0.0.0

module load fustr

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

1.0.7

module load gadgetviewer/1.0.7

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

5.0.0

module load gamos/5.0.0

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

1.1.0 and1.2.1

module load gatb

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

6.2, 7.1, 7.2

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

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

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

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

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

g16

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

for detailed citation requirements.

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.

0.91b

module load gblocks/0.91b

GNU Compiler Collection.

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

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

GCTA (Genome-wide Complex Trait Analysis)

1.26.0, 1.92.0

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

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

1.11.2, 2.3.1

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

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

7.6.1

module load gdb/7.6.1

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

1.2.0, 1.4.0

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

GNU Data Language (GDL).

0.9.6

module load gdl/0.9.6

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.

4.9.5, 4.10.01,4.10.02

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

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

1.7.1-i3

module load gemtools

GPL

Genome-wide Efficient Mixed Model Association

0.93

module load gemma/0.93

Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes.

4.21, 4.33

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

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.

2.22

module load gengetopt

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

1.3

module load genomemasker

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

1.5.9

module load genometools/1.5.9

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.

3.5.0

module load geos/3.5.0

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

0.9.2

module load gephi

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

1

None

GNU gettext package

0.19.8

module load gettext/0.19.8

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

2.1.2, 2.2.1

module load gflags/2.1.2 or module load gflags/2.2.1

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.

0.9-rc3

module load ghmm

LGPL

None

9.15

module load ghostscript/9.15

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

0.3.1

module load giremi

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

2.14.1, 2.16.2

module load git/2.14.1 or module load git/2.16.2

An OpenGL to PostScript printing library

1.4.0

module load gl2ps/1.4.0

None

2.34.0

module load glib/2.34.0

C++ implementation of the Google logging module.

0.3.3

module load glog/0.3.3

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

2017-06-20 00:00:00

module load gmap

GNU Multiple Precision Arithmetic Library.

4.3.2, 5.1.3, 6.1.0

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

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

4.1.5, 4.2

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

Gnuplot is a portable command-line driven graphing utility.

4.6.6, 5.0.0, 5.0.5

module load gnuplot/5.0.0 or module load gnuplot/5.0.5

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

1.8.3

module load golang

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

2.5

module load gperftools/2.5

A robust tool for the prediction of multiple lipid modification sites

1

module load gps-lipid

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

1.3.23

module load graphicsmagick/1.3.23

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

0.9.7

module load graphlan/0.9.7

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

0.9.7

module load graphlan/0.9.7

None

2.38.0

module load graphviz/2.38.0

The Genomic Rearrangement IDentification Software Suite

1.7.0, 2.0.1

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

Molecular dynamics simulation package.

4.6.7, 5.1, 5.1.4, 2016.2, 2018.2, 2019.1

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

Molecular dynamics simulation package.

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

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

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

1.16, 2.3

module load gsl/1.16 or module load gsl/2.3

Gordon-Text_utils-Library

0.6

module load gtextutils

The GNU Triangulated Surface Library

121130

module load gts/121130

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.

1.4.1

module load gubbins/1.4.1

LIBGUILE Project GNU extension language library.

1.8.2, 2.0.13

module load guile/1.8.2 or module load guile/2.0.13

GUROBI optimization solver

7.5.1, 8.0.1

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