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Software Overview

National Systems

For information on software available on Compute Canada's national systems please refer to the Available Software page on the Compute Canada User Documentation wiki. 

WestGrid Systems

On the WestGrid systems there is a core of common software, but due to user requirements or limitations of licensing or architecture, there are some differences in the programs offered at the various WestGrid sites. The tables below and the associated database summarize the majority of the software that has been added to the basic Linux environment.  Not every package has an entry in this database. For example, software that is licensed only to a specialized group of researchers may not be listed. Also, add-on modules for R, Perl and Python are less likely to be listed.

New software requests on WestGrid systems are no longer being accepted.  You are responsible for installing new software in your own directory.

Once you have located software of interest, either by scrolling through the full listing or by using the Search button and associated pull-down menus to filter the software by category or system, click on the software title.  That will lead to a page showing the software versions available on WestGrid systems as well as usage instructions for some packages.

The executables for commonly used software can usually be found on the PATH supplied by the default login environment at each WestGrid site. Some of the software is configured with the module command. Additional software, libraries, including files, documentation and other supporting files sometimes do not fit readily into a rigid installation scheme, but are usually installed under one or two standard directories for each site, such as /global/software.

All WestGrid Software

Software Category: Bioinformatics / Genomics Applications
Software Brief Description
BMTagger Best Match Tagger (BMTagger) is an efficient tool that discriminates between human reads and microbial reads without doing an alignment of all reads to the human genome.
IDBA-UD IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data
Kraken Kraken is a Taxonomic Sequence Classification System
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
PHAST (Phylogenic Analysis with Space/Time Models) PHAST (Phylogenic Analysis with Space/Time Models)
Trimmomatic A flexible read trimming tool for Illumina NGS data
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
ALLPATHS-LG Sequence assembly program.
BCFtools (VCF/BCF file manipulation) BCFtools is a set of utilities for manipulating Variant Call Format and related files.
bcl2fastq - Illumina BCL to FASTQ conversion utility bcl2fastq - Illumina BCL to FASTQ conversion utility
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BEDTools Utility suite for comparing genomic features.
biobambam biobambam - a set of tools for processing BAM format sequence files.
Biopython Collection of Python-based tools for bioinformatics.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
Bowtie Short read DNA sequence aligner.
Bowtie2 Short read DNA sequence aligner.
BUCKy (phylogenetic analysis) BUCKy - Bayesian phylogenetic analysis of gene tree concordance.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Celera Whole-Genome Shotgun Assembler Celera whole-genome shotgun sequence assembler and conversion utilities.
Clustal Omega Clustal Omega - Multiple protein sequence alignment
Coral Error correction software for DNA sequence analysis.
Cufflinks Transcript assembly from RNA-Seq data.
DIAMOND - sequence aligner Program for local aligments of translated nucleotide or amino acid sequences to protein references
DISCOVAR and DISCOVAR de novo - genome assembly DISCOVAR de novo whole genome shotgun assembler from 250-base Illumina PCR-free fragment reads.
ExaML/RAxML - Phylogenetic tree analysis Phylogenetic tree analysis.
FastQC Quality control tool for high throughput sequence data.
fastStructure (population genetics) Infer population structure from large SNP genotype data.
FASTX-Toolkit (sequence pre-processing) FASTX-Toolkit - command line tools for short read sequence data pre-processing.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
HMMER Homolog search and protein sequence alignments.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
IQ-TREE (phylogenetics) IQ-TREE is a phylogenetics package for inferring maximum likelihood trees.
JELLYFISH DNA substring (k-mer) counting.
kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees kSNP3 - Software to find single nucleotide polymorphisms in DNA sequences and estimate phylogenetic trees
MaSuRCA - whole genome assembler MaSuRCA whole genome assembler
MetAMOS MetAMOS - framework for genome assembly and analysis.
Mothur Bioinformatics software for microbial ecology.
Picard tools Java-based tools for manipulation of BAM (Binary sequence alignment map) data files.
PLINK Analysis of genotype/phenotype data.
RAPSearch (protein similarity search) RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search
Ray De novo genome assembly.
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
SGA Memory efficient de novo assembler of high-coverage short-read sequence data for large genomes
SHAPEIT (estimation of haplotypes) SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data
SNPTEST SNPTEST - Program for whole-genome SNP association studies
SOAPdenovo Short Oligonucleotide Analysis Package for Illumina GA short-read assembly.
SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
SPAdes Genome Assembler SPAdes - assembler for bacterial genomes
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
Tablet - Next Generation Sequence Assembly Visualization Tablet is a graphical viewer for next generation sequence assemblies and alignments.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
VCFtools a program package designed for working with VCF files
Velvet Package for genomic sequence assembly from short-read data.
WHAM/WHAMG - WHole-genome Alignment Metrics WHAM/WHAMG - WHole-genome Alignment Metrics for structural variant detection and association testing
Software Category: Chemistry and Biochemistry Applications
Software Brief Description
Open Babel Data conversion toolkit.
Software Category: Programming
Software Brief Description
Blitz++ C++ template library for dense vectors and multi-dimensional arrays.
Boost An eclectic collection of C++ libraries.
CMake Cross platform software build system
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
Git Version control system.
Jam Make replacement for C/C++ projects.
Java Java is a programming language and computing platform.
Mercurial Distributed version control system
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
Python Python is an interactive, object-oriented, extensible programming language.
Subversion An open source alternative to CVS for managing files for large development projects.
tvmet Tiny Vector Matrix library using Expression Templates.
Software Category: Files and Data
Software Brief Description
Climate Data Operators (CDO) A command line suite for manipulating and analysing climate data.
Emacs GNU version of this common text editor.
HDF 4 Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
NetCDF A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Szip A library for lossless compression of scientific data.
Vim An enhanced version of the vi text editor.
Software Category: Graphics
Software Brief Description
Circos Oriented towards genomic data display but can be applied to other data.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
ImageMagick Software suite for image format conversion and editing.
Matplotlib Python-based 2D (mostly) plotting library.
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
pdflib PDF file handling library ("PDFlib-Lite" for non-commercial use).
Qt Application and user interface development framework.
Software Category: Mathematical Libraries and Applications
Software Brief Description
BLAS Basic Linear Algebra Subprograms.
FFTW A widely-used FFT implementation.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
LAPACK Linear algebra subroutine package.
MATLAB Compiler Runtime (MCR) The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
MKL MKL is a vendor optimized numerical library with C and Fortran bindings for BLAS, LAPACK, ScaLAPACK, FFT, a sparse system solver, random number generators and vector versions of common mathematical functions.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
PARI/GP - computer algebra system PARI/GP - C library and interactive shell supporting calculations in number theory.
R Software environment and language for statistical data analysis.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
Software Category: UNIX Environment
Software Brief Description
64-bit Linux CentOS CentOS is an Enterprise-class Linux Distribution derived from sources freely provided to the public by a prominent North American Enterprise Linux vendor.
bash (default) Bash is a Unix shell.
csh The improved version of tcsh.
ksh It is an interactive command language that provides access to the UNIX system and to many other systems, on the many different computers and workstations on which it is implemented.
sh
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
Software Category: Other Applications
Software Brief Description
GDAL Geospatial Data Abstraction Library.
MATLAB A general purpose numerical package with a high-level programming language for linear algebra, signal processing, image processing, 2-D and 3-D graphics, etc.