Bioinformatics

This article is a draft

This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.

Software

See Available software for a list of bioinformatics applications on our systems. You can sort on 'Type', where bioinformatics software is categorized as 'bio'.

Some bioinformatics software is available as Python packages, which do not appear on the above list. See Available Python wheels for a list of Python "wheels" customized for Alliance clusters.

Data

Some genome databases are available on our clusters, in /cvmfs/ref.mugqic/genomes. Examine that directory and its subdirectories, e.g. with

[name@server ~]$ ls /cvmfs/ref.mugqic/genomes

or

[name@server ~]$ ls /cvmfs/ref.mugqic/genomes/species

Container Repository

The Bioinformatics National Team maintains a repository of Apptainer (formerly Singularity) containers which provide common workflows and those requiring preservation. Learn more at the Biorepo_Containers page.