BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target), such as the human reference genome.
It implements three different algorithms, all based on Burrows-Wheeler Transform (BWT).
The first algorithm BWA-backtrack is designed for short queries up to ~200bp with low error rate (<3%).
It does gapped global alignment w.r.t. queries, supports paired-end reads, and is one of the fastest short read alignment algorithms to date while also visiting suboptimal hits.
The second algorithm BWA-SW is designed for long reads (ranging from 70bp to 1Mbp) with more errors.
It performs heuristic Smith-Waterman-like alignment to find high-scoring local hits (and thus chimera).
On low-error short queries, BWA-SW is slower and less accurate than the first algorithm, but on long queries, it is better.
The latest algorithm BWA-MEM is similar to BWA-SW.
It is generally recommended for high-quality queries as it is faster and more accurate than BWA-SW.
BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.
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