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, Maker, 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

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

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

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

Library for high performance linear algebra computations.

3.5.0, 3.8.0

module load lapack/3.5.0xxx (where xxx is the version)

coming soon

NoneMAKER is a portable and easily configurable genome annotation pipeline.

2.31.8, 2.31.10

module load maker/2.31.8xxx (where xxx is the version)

coming soon

Pipeline to generate complete public health microbiology reports from sequenced isolates.

1.01, 1.2, 1.20-test, 1.20, 2.0

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

coming soon

PIPITS is an automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences from the Illumina sequencing platform.

1.2.0, 2.2

module load pipits/1.2.0xxx (where xxx is the version)

coming soon

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

1.11, 1.13.3

module load prokka/1.11xxx (where xxx is the version)

coming soon

STAR RNA-seq aligner.

2.4.0j, 2.5.2a, 2.6.1b

module load star/2.4.0j or module load star/2.5.2axxx (where xxx is the version)

coming soon