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

Abaqus, Ansys, AnsysEM, CGNS, 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, barrnap, BASE, Basespace, 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, Cd-Hit, Centrifuge, Chimera, Chimeraslayer, ChunkChromosome, Clonalframeml, Clustal Omega, Clustal W/X, Codonphyml, Cortex, Crest, Cufflinks, Cutadapt, Delly, Diamond, Drive5, Ea-Utils, EDirect, Emboss, EMMAX, EPA-ng, Epacts, EVidenceModeler, ExaBayes, EXCAVATOR2tool, exonerate, Falcon, Falcon-Unzip, Fastml, fastPHASE, FastQC, Fasttree, Fastx, Flash, fqgrep, fqtools, FRANz, freebayes, funannotate, gatb, Gatk, Gblocks, gcta, gem-tools, Gemma, GeneMark-ES, Genomemasker, GenomeTools, Gess, giremi, gmap, GraPhlAn, GraPhlAn, GRIDSS, Gubbins, Haddock, hapcut, Hapcut, Hapflow, haplotyper, Haploview, Hapsembler, Hh-Suite, HiC-bench, HISAT2, hlascan, Hmmer, Homer, hotspotter, Htslib, I-Tasser, Idba, idp, Igvtools, IMPUTE2, Infernal, IQ-TREE, Is_Mapper, ITSx, Iva, Jaspa, Jellyfish, Juicer, Kalign, kallisto, Kat, kentutils, Kmc, Kraken, Kraken2, LAST, libmaus2, lighter, Lofreq, longranger, lordec, Lumpy-Sv, MACH, MaCH-Admix, MAFFT, Magic-BLAST, Maker, Manta, MARVEL, Mash, MATAM, Mauve, Medusa, Megacc, Megahit, megan, Meme, MetaPhlAn2, Metatissue, Methpipe, MethylDackel, Migrate-N, minced, Minimac2, Minimac4, Minimap2, Mira, Mirdeep2, Mlst, Mothur, Mrbayes, Mugsy, Mummer3, Mummer4, Mutect, Mykrobe-Predictor, NanoOk, Nanopolish, NCBI C++ Toolkit, Newick-Utils, Norgal, Nullarbor, oases, Paml, pandaseq, Pblat, Pear, PennCNV, pgdspider, phase, Pheniqs, PHYLIP, Phyml, Picard, Pilon, Pindel, Pipits, PLINK, PneumoCaT, Prank, Preseq, Prinseq, Prodigal, Prokka, ProteinOrtho, PSIPRED, PSMC, Purge Haplotigs, Qiime, Qorts, Qualimap, Quast, Ragout, Ray, Rdpclassifier, Reddog, Repeatmasker, Repeatmodeler, RepeatScout, Rmats, Rnammer, Roary, Rosetta, Rsem, salmon, sam2bam, Sambamba, Samblaster, samclip, Samtools, scotti, seqOutBias, Seqtk, sff2fastq, Sga, SHAPEIT, Shorah, ShortStack, shovill, Sibelia, Signalp, SKESA, Smalt, Smrt, Snippy, snp-dists, SNPhylo, SOAPdenovo2, SortMeRNA, Spades, SpeedSeq, Sratoolkit, STACKS, Stampy, Star, Strainseeker, Strelka, Stringtie, subread, Subread, Supernova, Surpi, Svtyper, Tabix, Tbl2Asn, Tophat, Tracer, Transdecoder, trimAl, Trimgalore, Trimmomatic, Trinity, Trinotate, tRNAscan-SE, UCSC Genome Browser, Usearch, Varscan, VaST, vcf2diploid, Vcftools, Velvet, ViennaRNA, Vmatch, Vsearch, WALT, Wgs, wgsim, XP-EHH

afni, Amos, ANTs, ASHS, c3d, 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, Readosm, 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, Suitesparse

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

Cairo, cairomm, Circos, Ffmpeg, FreeGLUT, Freetype, Ghostscript, Gnuplot, Graphicsmagick, Idl, Imagej, Imagemagick, Imp, Jasper, Libgd, Libjpeg, Libpng, libQGLViewer, MayaVi, OpenJPEG, 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, 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, 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, Suitesparse

emacs

Gcc, Intel, Java, Pgi

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

Gdb, Re2, Valgrind

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

Macaulay2, Mathematica, Matlab, Mcr, petsc, PHCpack, SAS

MySQL, Pgsql, Sqlite

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

1.0.0-rc3

module load caffe-3d

coming soon

ABAQUS Finite Element Analysis products.

6.14-1, 2016

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

coming soon

Mass screening of contigs for antibiotic resistance genes.

0.3, 0.5, 0.8

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

coming soon

De novo genome sequence assembler.

1.9.0

module load abyss/1.9.0

coming soon

De novo genome sequence assembler.

1.9.0, 2.0.2

module load abyss-mpi/1.9.0

coming soon

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

coming soon

AFNI (Analysis of Functional NeuroImages)

17.2.02

module load afni

None

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

0.9.6

module load afterqc/0.9.6

coming soon

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

2.1.0

module load ag/2.1.0

coming soon

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

3242011

module load aligngraph/3242011

coming soon

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

coming soon

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

52488

module load allpathslg/52488

coming soon

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

coming soon

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

0.0.0

module load amrplusplus

coming soon

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

coming soon

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

coming soon

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

coming soon

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)

coming soon

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

170, 172, 180, 181, 182, 190, 191, 192

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

coming soon

A unified platform for electromagnetic, circuit and system simulation.

170, 181, 182

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

coming soon

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)

coming soon

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

2.2.0

module load ants

None

tRNA (and tmRNA) detection.

1.2.36

module load aragorn/1.2.36

coming soon

An ANSI C library for parsing GNU style command line arguments

13

module load argtable2

coming soon

A fast download utility.

1.25.0

module load aria2/1.25.0

coming soon

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

coming soon

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

coming soon

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

coming soon

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

coming soon

Automatic Segmentation of Hippocampal Subfields (ASHS)

20170223

module load ashs

None

Automatically Tuned Linear Algebra Software.

3.10.2, 3.10.3

module load atlas/3.10.2 or module load atlas 3.10.3

coming soon

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

coming soon

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

2.69

module load autoconf/2.69

coming soon

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

coming soon

count DNA sequence reads in BAM files

0.8.0

module load bam-readcount

None

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

coming soon

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

coming soon

Bayesian Analysis of Population Structure.

6

module load baps/6

coming soon

Barrnap predicts the location of ribosomal RNA genes in genomes.

0.6

module load barrnap

None

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

1.0

module load base/1.0

coming soon

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

coming soon

BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes

3.0.4

module load bayesass

coming soon

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

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

coming soon

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

coming soon

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

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

coming soon

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

coming soon

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)

coming soon

BEDOPS high-performance genomic feature operations

2.4.30

module load bedops/2.4.30

coming soon

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)

coming soon

GNU Binary file utilities.

2.26, 2.30

module load binutils/2.26 or module load binutils/2.30

coming soon

Tools for early stage alignment file processing

2.0.72

module load biobambam2

None

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

coming soon

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

1

module load biopieces/1

coming soon

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

0.19.0

module load bismark/0.19.0

coming soon

None

3

module load bison/3

coming soon

None

3.5.0

module load blas/3.5.0

coming soon

The PacBio long read aligner

1.3.1

module load blasr/1.3.1

coming soon

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

coming soon

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)

coming soon

Web tools to help understand the human genome.

3.6

module load blat/3.6

coming soon

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

1.0

module load blobtools

coming soon

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)

coming soon

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

coming soon

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

coming soon

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

3.3a

module load bpp/3.3a

coming soon

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

coming soon

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

coming soon

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

coming soon

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)

coming soon

Bam and Variant Analysis Tools.

1.6

module load bvatools/1.6

coming soon

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, 0.7.17

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

coming soon

None

1.0.6

module load bzip2/1.0.6

coming soon

Convert3D Medical Image Processing Tool

1.0.0

module load c3d

None

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

coming soon

A New Lightweight, Modular, and Scalable Deep Learning Framework

0.8.1

module load caffe2

coming soon

None

1.12.18, 1.14.10

module load cairo/1.12.18 or module load cairo/1.14.10

coming soon

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

1.15.3

module load cairomm

None

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)

coming soon

CAP3 Sequence Assembly Program.

20150421

module load cap3/20150421

coming soon

None

3.5.0

module load cblas/3.5.0

coming soon

A program for clustering and comparing protein or nucleotide sequences.

4.6.1, 4.6.5

module load cd-hit/4.6.1

coming soon

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

None

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

coming soon

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

module load cfitsio

None

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)

coming soon

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

coming soon

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

coming soon

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

coming soon

ChunkChromosome is a helper utility for minimac and MaCH.

27-05-14

module load chunkchromosome

coming soon

Flexible and automatable circular data visualisation.

0.69-3

module load circos/0.69-3

coming soon

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)

coming soon

Efficient inference of recombination in bacterial genomes.

1

module load clonalframeml/1

coming soon

Multiple alignment of nucleic acid and protein sequences

1.2.4

module load clustal-omega

coming soon

Multiple alignment of nucleic acid and protein sequences

2.1

module load clustal

coming soon

Cross-platform, open-source build system.

3.0.1, 3.4.0, 3.9.4, 3.11.4

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

coming soon

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

coming soon

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

coming soon

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

coming soon

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

coming soon

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

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

coming soon

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

coming soon

Transcriptome assembly and differential expression analysis for RNA-Seq.

2.2.1

module load cufflinks/2.2.1

coming soon

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

7.59.0

module load curl/7.59.0

coming soon

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

coming soon

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.

coming soon

None

1.8.16

module load dbus/1.8.16

coming soon

None

0.104

module load dbus-glib/0.104

coming soon

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

1.0.20170624

module load dcm2niix

None

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

3.6.1

module load dcmtk/3.6.1

coming soon

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

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

coming soon

Accelerated BLAST compatible local sequence aligner.

0.8.28.90, 0.9.10

module load diamond/0.8.28.90

coming soon

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

4.07

module load dlpoly/4.07

coming soon

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

coming soon

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

0

module load drive5/0

coming soon

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

coming soon

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

coming soon

Amazon Elastic Compute Cloud tools.

1.7.5.1

module load ec2-api-tools/1.7.5.1

coming soon

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)

coming soon

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

coming soon

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)

coming soon

An extensible and customisable text editor

7.59.0

module load curl/7.59.0

coming soon

EMBOSS: The European Molecular Biology Open Software Suite.

6.6.0

module load emboss/6.6.0

coming soon

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

20120210

module load emmax/20120210

coming soon

Massively parallel phylogenetic placement of genetic sequences

0.2.1-beta

module load epa-ng

coming soon

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

coming soon

None

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

module load epimine/xxx (where xxx represents

coming soon

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

coming soon

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

coming soon

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

1

module load exciting

coming soon

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

coming soon

FALCON: experimental PacBio diploid assembler

0.1, 0.5

module load falcon/0.1 or module load falcon/0.5

coming soon

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

52016

module load falcon-unzip/52016

coming soon

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

coming soon

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

1.4.8

module load fastphase

None

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)

coming soon

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

2.1.8, 2.1.9

module load fasttree/2.1.8 or module load fasttree/2.1.9

coming soon

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

coming soon

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

coming soon

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)

coming soon

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

coming soon

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

coming soon

None

2.5.39

module load flex/2.5.39

coming soon

None

2.11.92

module load fontconfig/2.11.92

coming soon

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

0.4.4

module load fqgrep

None

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

2.1

module load fqtools/2.1

coming soon

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

2.0.0

module load franz

coming soon

Bayesian haplotype-based polymorphism discovery and genotyping.

1.0.2-33, 1.2.0

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

coming soon

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)

coming soon

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)

coming soon

None

2.5.5

module load freetype/2.5.5

coming soon

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

coming soon

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

5.0.8, 5.0.9

module load fsl/5.0.8 or module load fsl/5.0.9

coming soon

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

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

1.0.7

module load gadgetviewer/1.0.7

coming soon

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

coming soon

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

None

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)

coming soon

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

3.3.0, 3.6.0, 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)

coming soon

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

g16

module load gaussian

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

coming soon

GNU Compiler Collection.

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

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

coming soon

GCTA (Genome-wide Complex Trait Analysis)

1.26.0

module load gcta

None

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)

coming soon

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

7.6.1

module load gdb/7.6.1

coming soon

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

module load gdc-client/1.2.0

coming soon

GNU Data Language (GDL).

0.9.6

module load gdl/0.9.6

coming soon

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)

coming soon

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

coming soon

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

coming soon

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

1.3

module load genomemasker

None

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

coming soon

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

coming soon

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

0.9.2

module load gephi

coming soon

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

1

None

coming soon

GNU gettext package

0.19.8

module load gettext/0.19.8

coming soon

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

coming soon

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

coming soon

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

None

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

coming soon

An OpenGL to PostScript printing library

1.4.0

module load gl2ps/1.4.0

coming soon

None

2.34.0

module load glib/2.34.0

coming soon

C++ implementation of the Google logging module.

0.3.3

module load glog/0.3.3

coming soon

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

None

GNU Multiple Precision Arithmetic Library.

4.3.2, 5.1.3, 6.1.0

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

coming soon

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

coming soon

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

1.8.3

module load golang

None

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

coming soon

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

coming soon

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

coming soon

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

coming soon

None