General Description

BWA Version 0.6.2

 **This version is recommended for aln/sampe/samse.  bwa version 1.8.3 is recommended for mem**

Basic Usage

module load bio #to load all bio modules
module load bio/bwa/0.6.2 #to load bwa alone

Useful Options

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.6.2-r126
Contact: Heng Li <>

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
         fastmap       identify super-maximal exact matches

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

Further Information

See the official website: [http:// ]