Bowtie2

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Bowtie2

http://bowtie-bio.sourceforge.net/bowtie2
ultrafast memory-efficient short read aligner

is 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


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Licensing

LicenseVerified byVerified onNotes
License:GPLv3orlaterDebian20 March 2013
License: GPL-3.0+

This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>

On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-

licenses/GPL-3".
ZlibDebian20 March 2013
License: Zlib

This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software.

Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions:

1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source

distribution.
OtherDebian20 March 2013
License:

This file contains an implementation of the algorithm presented in "Faster Suffix Sorting" by N. Jesper Larsson (jesper@cs.lth.se) and Kunihiko Sadakane (sada@is.s.u-tokyo.ac.jp).

This software may be used freely for any purpose. However, when distributed, the original source must be clearly stated, and, when the source code is distributed, the copyright notice must be retained and any alterations in the code must be clearly marked.

No warranty is given regarding the quality of this software.



Leaders and contributors

Contact(s)Role
Ben Langmead contact


Resources and communication

AudienceResource typeURI
Downloadhttp://sourceforge.net/projects/bowtie2-bio/files/bowtie2/


Software prerequisites



Entry



Date 2013-03-20
Source Debian import
Source link http://packages.debian.org/sid/bowtie2

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"contact" is not in the list (Maintainer, Contributor, Developer, Sponsor, Unknown) of allowed values for the "Role" property.






Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the page “GNU Free Documentation License”.

The copyright and license notices on this page only apply to the text on this page. Any software or copyright-licenses or other similar notices described in this text has its own copyright notice and license, which can usually be found in the distribution or license text itself.