From HPC wiki


bwa 0.5.9-r16 is installed across all HPC nodes.


At this time, bwa can be called without the need for an environment module on any of the compute nodes.

[asrini@consign ~]$ bsub -Is bash

[asrini@node061 ~]$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.5.9-r16
Contact: Heng Li <lh3@sanger.ac.uk>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         pac_rev       generate reverse PAC
         bwt2sa        generate SA from BWT and Occ
         pac2cspac     convert PAC to color-space PAC
         stdsw         standard SW/NW alignment

Other Pages