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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
WHAM/WHAMG - WHole-genome Alignment Metrics WHAM/WHAMG - WHole-genome Alignment Metrics for structural variant detection and association testing
Velvet Package for genomic sequence assembly from short-read data.
VCFtools a program package designed for working with VCF files
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
Trimmomatic A flexible read trimming tool for Illumina NGS data
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
Tablet - Next Generation Sequence Assembly Visualization Tablet is a graphical viewer for next generation sequence assemblies and alignments.
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
SPAdes Genome Assembler SPAdes - assembler for bacterial genomes
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.
SOAPdenovo Short Oligonucleotide Analysis Package for Illumina GA short-read assembly.
SNPTEST SNPTEST - Program for whole-genome SNP association studies
SHAPEIT (estimation of haplotypes) SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data
SGA Memory efficient de novo assembler of high-coverage short-read sequence data for large genomes
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
Ray De novo genome assembly.
RAPSearch (protein similarity search) RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search
PLINK Analysis of genotype/phenotype data.
Picard tools Java-based tools for manipulation of BAM (Binary sequence alignment map) data files.
PHAST (Phylogenic Analysis with Space/Time Models) PHAST (Phylogenic Analysis with Space/Time Models)
Mothur Bioinformatics software for microbial ecology.
MetAMOS MetAMOS - framework for genome assembly and analysis.
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
MaSuRCA - whole genome assembler MaSuRCA whole genome assembler
kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees kSNP3 - Software to find single nucleotide polymorphisms in DNA sequences and estimate phylogenetic trees
Kraken Kraken is a Taxonomic Sequence Classification System
JELLYFISH DNA substring (k-mer) counting.
IQ-TREE (phylogenetics) IQ-TREE is a phylogenetics package for inferring maximum likelihood trees.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
IDBA-UD IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data
HMMER Homolog search and protein sequence alignments.
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
FASTX-Toolkit (sequence pre-processing) FASTX-Toolkit - command line tools for short read sequence data pre-processing.
fastStructure (population genetics) Infer population structure from large SNP genotype data.
FastQC Quality control tool for high throughput sequence data.
ExaML/RAxML - Phylogenetic tree analysis Phylogenetic tree analysis.
DISCOVAR and DISCOVAR de novo - genome assembly DISCOVAR de novo whole genome shotgun assembler from 250-base Illumina PCR-free fragment reads.
DIAMOND - sequence aligner Program for local aligments of translated nucleotide or amino acid sequences to protein references
Cufflinks Transcript assembly from RNA-Seq data.
Coral Error correction software for DNA sequence analysis.
Clustal Omega Clustal Omega - Multiple protein sequence alignment
Celera Whole-Genome Shotgun Assembler Celera whole-genome shotgun sequence assembler and conversion utilities.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
BUCKy (phylogenetic analysis) BUCKy - Bayesian phylogenetic analysis of gene tree concordance.
Bowtie2 Short read DNA sequence aligner.
Bowtie Short read DNA sequence aligner.
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.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
Biopython Collection of Python-based tools for bioinformatics.
biobambam biobambam - a set of tools for processing BAM format sequence files.
BEDTools Utility suite for comparing genomic features.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
bcl2fastq - Illumina BCL to FASTQ conversion utility bcl2fastq - Illumina BCL to FASTQ conversion utility
BCFtools (VCF/BCF file manipulation) BCFtools is a set of utilities for manipulating Variant Call Format and related files.
ALLPATHS-LG Sequence assembly program.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
Software Category: Files and Data
Software
Brief Description
Vim An enhanced version of the vi text editor.
Szip A library for lossless compression of scientific data.
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.
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
HDF 4 Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.
Emacs GNU version of this common text editor.
Climate Data Operators (CDO) A command line suite for manipulating and analysing climate data.
Software Category: Programming
Software
Brief Description
tvmet Tiny Vector Matrix library using Expression Templates.
Subversion An open source alternative to CVS for managing files for large development projects.
Python Python is an interactive, object-oriented, extensible programming language.
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
Mercurial Distributed version control system
Java Java is a programming language and computing platform.
Jam Make replacement for C/C++ projects.
Git Version control system.
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
CMake Cross platform software build system
Boost An eclectic collection of C++ libraries.
Blitz++ C++ template library for dense vectors and multi-dimensional arrays.
Software Category: UNIX Environment
Software
Brief Description
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
sh
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.
csh The improved version of tcsh.
bash (default) Bash is a Unix shell.
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.
Software Category: Mathematical Libraries and Applications
Software
Brief Description
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
R Software environment and language for statistical data analysis.
PARI/GP - computer algebra system PARI/GP - C library and interactive shell supporting calculations in number theory.
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
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.
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.
LAPACK Linear algebra subroutine package.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
FFTW A widely-used FFT implementation.
BLAS Basic Linear Algebra Subprograms.
Software Category: Graphics
Software
Brief Description
Qt Application and user interface development framework.
pdflib PDF file handling library ("PDFlib-Lite" for non-commercial use).
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
Matplotlib Python-based 2D (mostly) plotting library.
ImageMagick Software suite for image format conversion and editing.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Circos Oriented towards genomic data display but can be applied to other data.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
Open Babel Data conversion toolkit.
Software Category: Other Applications
Software
Brief Description
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.
GDAL Geospatial Data Abstraction Library.