Burrows-Wheeler Aligner (bwa) is a program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short, which works for query sequences shorter than 200 bp and BWA-SP which works for longer sequences, up to around 100 kbp. Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates.

The BWA package is prepared by Debian-Med and can be installed in Bio-Linux by typing:

For further information about BWA refer to the remote documentation