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:
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:
or check the BWA manual: http://bio-bwa.sourceforge.net/bwa.shtml.
The page Running BWA Commands shows how to run BWA on HCC.