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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 | 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 | Brief Description | |
|---|---|---|
| Open Babel | Data conversion toolkit. |
| 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 | 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 | 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 | 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 | 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 | 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. |