BWA is a software package for mapping DNA sequences against a large
reference genome, such as the human genome. It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
designed for Illumina sequence reads up to 100bp, while the other two
are for longer sequences ranging from 70bp to a few megabases. BWA-MEM
and BWA-SW share similar features such as the support of long reads
and chimeric alignment, but BWA-MEM, which is the latest, is generally
recommended, as it is faster and more accurate. BWA-MEM also has
better performance than BWA-backtrack for 70-100bp Illumina reads.

For all algorithms, BWA first needs to construct the FM-index for the
reference genome (the "bwa index" command). Alignment algorithms are
invoked with different sub-commands: "bwa aln/samse/sampe" for
BWA-backtrack, "bwa bwasw" for BWA-SW, and "bwa mem" for the BWA-MEM
algorithm.