BWA

BWA is an efficient read alignment package based on a backward search with Burrows-Wheeler Transform (BWT). It allows the alignment of short sequencing reads against a large reference sequence, such as the human genome while allowing mismatches and gaps. This software tool is developed to meet the demand for fast and accurate read alignment programs, especially for the enormous amount of short reads generated by new DNA sequencing technologies. The first generation of hash table-based methods, including MAQ, was accurate, feature-rich, and fast enough to align short reads from a single individual. However, MAQ is unsuitable for aligning longer reads where indels may occur frequently. Its speed is a concern when scaling up the alignment to the re-sequencing of hundreds of individuals.

BWA supports base space reads, e.g., from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on simulated and real data suggest that BWA is approximately 10-20x faster than MAQ while achieving similar accuracy. It outputs alignment in the new standard SAM (Sequence Alignment/Map) format, making it easier for downstream analyses such as variant calling to be performed with the open-source SAMtools software package.