BWA (Burrows-Wheeler Aligner) is a software package for mapping relatively short nucleotide sequences against a long reference sequence. BWA is slower than Bowtie, but allows indels in the alignment.

The basic usage of BWA is:

$ bwa COMMAND [options]
where COMMAND is one of the available BWA commands:

  • index: index sequences in the FASTA format
  • mem: BWA-MEM algorithm
  • fastmap: identify super-maximal exact matches
  • pemerge: merge overlapping paired ends (EXPERIMENTAL)
  • 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
  • bwt2sa: generate SA from BWT and Occ

BWA supports three alignment algorithms, mem, bwasw, and aln/samse/sampe. bwa mem is the latest algorithm, and is faster, more accurate and has better performance than bwa bwasw and bwa aln/samse/sampe. Therefore, if there are not any specific reasons, bwa mem is recommended for first-time users.

For detailed description and more information on a specific command, just type:

$  bwa COMMAND
or check the BWA manual.

The page Running BWA Commands shows how to run BWA on HCC.