BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.
- Support Illumina, SOLiD, 454, Sanger reads, PacBio reads and assembly contigs
- Gapped alignment and paired-end mapping
- Accurate, fast and lightweight
Only consider BWA version 0.6.2 as the latest sufficiently tested and stable version. That said, this is a very good application for aligning short sequencing reads.