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]
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.