Bwa is a software package for mapping low-divergent 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 rest two for longer sequences ranged from 70bp to 1mbp. bwa-mem and bwa-sw share similar features such as long-read support and split alignment, but bwa-mem, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. bwa-mem also has better performance than bwa-backtrack for 70-100bp illumina reads.

this package contains the source files for use in other programs.