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