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.
