MOTIVATION: The enormous amount of short reads generated by the new DNA 
sequencing technologies call for the development of fast and accurate read 
alignment programs. A first generation of hash table-based methods has been 
developed, including MAQ, which is accurate, feature rich and fast enough to 
align short reads from a single individual. However, MAQ does not support gapped 
alignment for single-end reads, which makes it unsuitable for alignment of 
longer reads where indels may occur frequently. The speed of MAQ is also a 
concern when the alignment is scaled up to the resequencing of hundreds of 
individuals.
RESULTS: We implemented Burrows-Wheeler Alignment tool (BWA), a new read 
alignment package that is based on backward search with Burrows-Wheeler 
Transform (BWT), to efficiently align short sequencing reads against a large 
reference sequence such as the human genome, allowing mismatches and gaps. BWA 
supports both base space reads, e.g. from Illumina sequencing machines, and 
color space reads from AB SOLiD machines. Evaluations on both simulated and real 
data suggest that BWA is approximately 10-20x faster than MAQ, while achieving 
similar accuracy. In addition, BWA outputs alignment in the new standard SAM 
(Sequence Alignment/Map) format. Variant calling and other downstream analyses 
after the alignment can be achieved with the open source SAMtools software 
package.
AVAILABILITY: http://maq.sourceforge.net.