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|sw summary=Bowtie is an ultrafast, memory-efficient short read aligner.
|bio method=Mapping, Burrows-Wheeler, FM-Index
|created by=Ben Langmead, Cole Trapnell, Mihai Pop, Steven Salzberg|created at=University of Maryland, Johns Hopkins University|maintained=Yes
|input format=FASTQ,
|output format=SAM
= Alternatives =
[[BWA]] supports indels, but is a bit slower.
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