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Application data

Created by Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg
Principal bioinformatics method(s) Read mapping, Genome indexing (Burrows-Wheeler)
Created at University of Maryland, Johns Hopkins University
Maintained? Yes
Input format(s) FASTQ
Output format(s) SAM
Software version 1.1.2
Operating system(s) Mac OS X, Linux, Windows
Contact: [email protected]

Summary: Bowtie is an ultrafast, memory-efficient short read aligner.

Bowtie aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: 1.3 GB for the human genome. It supports alignment policies equivalent to Maq and SOAP but is much faster: about 35x faster than Maq and over 350x faster than SOAP when aligning to the human genome.



  • Bowtie1 only handles a limited number of indels. Bowtie 2 has no limit and can handle any number of indels as well as very long reads.


BWA and SOAP2 are the most popular alternatives. BWA is about 25% slower and slightly less sensitive. SOAP2 is comparable in speed but considerably less sensitive (aligning fewer reads).



  1. Langmead B, Trapnell C, Pop M, Salzberg SL.. 2009. Genome Biology
  2. Benjamin Langmead, Steven L. Salzberg. 2012. Nature Methods

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