Difference between revisions of "Bedtools"

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(Debian import)
 
(Updated version, homepage, download links)
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{{Entry
 
{{Entry
|Status=
 
|User level=
 
|Submitted by=Debian import
 
|Computer languages=C++
 
 
|Name=Bedtools
 
|Name=Bedtools
|Submitted date=2013-03-20
 
 
|Short description=suite of utilities for comparing genomic features
 
|Short description=suite of utilities for comparing genomic features
|VCS checkout command=
 
 
|Full description=The BEDTools utilities allow one to address common genomics tasks
 
|Full description=The BEDTools utilities allow one to address common genomics tasks
 
such as finding feature overlaps and computing coverage. The
 
such as finding feature overlaps and computing coverage. The
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The groupBy utility is distribued in the filo package.
 
The groupBy utility is distribued in the filo package.
|Component programs=
+
|Homepage URL=https://github.com/arq5x/bedtools2
|Homepage URL=http://code.google.com/p/bedtools/
+
|Computer languages=C++
 +
|Version identifier=2.26.0
 +
|Version date=2016/07/06
 +
|Version status=stable
 +
|Version download=https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz
 +
|Last review by=Tim Howes
 +
|Last review date=2016/10/07
 +
|Submitted by=Debian import
 +
|Submitted date=2013-03-20
 +
|Status=
 
|Is GNU=No
 
|Is GNU=No
}}
 
{{Import
 
|Date=2013-03-20
 
|Source=Debian import
 
|Source link=http://packages.debian.org/sid/bedtools
 
 
}}
 
}}
 
{{Project license
 
{{Project license
|License verified date=2013-03-20
+
|License=GPLv2
|License verified by=Debian
 
 
|License copyright=© © 2009,2010,2011 Aaron Quinlan
 
|License copyright=© © 2009,2010,2011 Aaron Quinlan
 
© © 2010 - Assaf Gordon, CSHL
 
© © 2010 - Assaf Gordon, CSHL
 
+
|License verified by=Debian
|License=GPLv2
+
|License verified date=2013-03-20
 
|License note=License: GPL-2
 
|License note=License: GPL-2
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
 +
|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2009, 2010, 2011 - Aaron Quinlan
 
 
|License=Other
 
 
|License note=License: under-the-MIT-license
 
|License note=License: under-the-MIT-license
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=GPLv2
 +
|License copyright=© © 2010 Erik Garrison <erik.garrison@bc.edu>
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2010 Erik Garrison <erik.garrison@bc.edu>
 
 
|License=GPLv2
 
 
|License note=License: GPL-2
 
|License note=License: GPL-2
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
 +
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
 
 
|License=Other
 
 
|License note=License: MIT
 
|License note=License: MIT
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=Other
 +
|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2001  Deepak Bandyopadhyay, Lutz Kettner
 
 
|License=Other
 
 
|License note=License: LGPL-2.1
 
|License note=License: LGPL-2.1
  
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}}
 
}}
 
{{Project license
 
{{Project license
 +
|License=BSD_2Clause
 +
|License copyright=© © 2007-2010 by the Sphinx team
 +
|License verified by=Debian
 
|License verified date=2013-03-20
 
|License verified date=2013-03-20
|License verified by=Debian
 
|License copyright=© © 2007-2010 by the Sphinx team
 
 
|License=BSD_2Clause
 
 
|License note=License: BSD-2-clause
 
|License note=License: BSD-2-clause
  
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}}
 
}}
 
{{Resource
 
{{Resource
|Resource URL=http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz
 
 
|Resource kind=Download
 
|Resource kind=Download
 +
|Resource URL=https://github.com/arq5x/bedtools2/releases/latest
 +
}}
 +
{{Software category}}
 +
{{Featured}}
 +
{{Import
 +
|Date=2013-03-20
 +
|Source=Debian import
 +
|Source link=http://packages.debian.org/sid/bedtools
 
}}
 
}}

Revision as of 12:56, 7 October 2016


[edit]

Bedtools

https://bedtools.readthedocs.io/en/latest/
Suite of utilities for comparing genomic features.

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.

The groupBy utility is distribued in the filo package.





Licensing

License

Verified by

Verified on

Notes

License

GPLv2

Verified by

Debian

Verified on

20 March 2013

Verified by

Debian

Verified on

20 March 2013

License

Expat

Verified by

Debian

Verified on

20 March 2013

Verified by

Debian

Verified on

20 March 2013




Leaders and contributors

Resources and communication

AudienceResource typeURI
Mailing Listhttps://groups.google.com/forum/?fromgroups#!forum/bedtools-discuss
VCS Repository Webviewhttps://github.com/arq5x/bedtools2
Debian (Ref)https://tracker.debian.org/pkg/bedtools
Generalhttps://www.biostars.org/t/bedtools/


Software prerequisites




Entry




























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

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