An ultrafast, memory-efficient short read aligner that aligns short DNA sequences to the human genome at a rate of about 25 million reads per hour on a typical workstation with 2 GB of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.1 GB for the human genome.

Steven Salzberg has been nominated for the 2013 Benjamin Franklin Award in the Life Sciences. This is a humanitarian/bioethics award presented to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. More information on the award can be found at