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Examples for bowtie2,

an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.

Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

This package provides some example data to work with bowtie2.

Package version:2.0.0-beta6-3


bowtie2 (2.0.0-beta6-3) unstable; urgency=low

  * normalized architecture detection.
    For example kfreebsd-amd64 is detected as an amd64 architecture 
    and msse flag is set.(Previous commit was wrong) (Closes: #673159)

 -- Alexandre Mestiashvili <>  Fri, 01 Jun 2012 21:58:49 +0200

bowtie2 (2.0.0-beta6-2) unstable; urgency=low

  * debian/rules normalized output of


Bowtie 2 NEWS

Bowtie 2 is now available for download from the project website,  2.0.0-beta1 is the first version released to
the public and 2.0.0-beta6 is the latest version.  Bowtie 2 is licensed under
the GPLv3 license.  See `COPYING' file for details.

Reporting Issues

Please report any issues using the Sourceforge bug tracker:



Upstream-Name: Bowtie2
Upstream-Contact: Ben Langmead <>

Files: *
Copyright: © 2009-2010 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg
License: GPL-3.0+

Files: ls.h
Copyright: © 1999, N. Jesper Larsson
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