|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|
|Operating system(s)||Mac OS X, Linux, Windows|
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.
- Langmead B, Trapnell C, Pop M, Salzberg SL.. 2009. Genome Biology
- Benjamin Langmead, Steven L. Salzberg. 2012. Nature Methods
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