Bowtie specifications

Unique identifier:
OMICS_00653
Software type:
Toolkit/Suite
Restrictions to use:
None
Output format:
SAM, FAI
Programming languages:
C, C++
Computer skills:
Advanced
Stability:
Stable
Alternative name:
Bowtie2
Interface:
Command line interface
Input format:
FASTA, FASTQ, FA
Operating system:
Unix/Linux
License:
Artistic License version 2.0
Version:
1.2.2
Maintained:
Yes

Subtools

  • bowtie-build
  • bowtie-inspect
  • bowtie

versioning

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No versioning.

Bowtie distribution

download

Bowtie support

Documentation

Maintainer

  • Ben Langmead <>

forum

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Credits

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Publications

Institution(s)

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA

Funding source(s)

Supported in part by US National Institutes of Health grants R01-HG006102 and R01-GM083873 and an Amazon Web Services in Education Research grant in July 2011.

User review

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4 user reviews

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4 user reviews

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Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

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Bowtie is the most commonly used short read aligner after BWA. Tophat2 in tuxedo suite is based on bowtie.

Rytis Liaudanskas's avatar image Rytis Liaudanskas's country flag

Rytis Liaudanskas

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Great read mapper.

Claudia Armenise Quartz Bio's avatar image

Claudia Armenise Quartz Bio

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A very useful read mapper, bowtie performs full-length mapping whereas bowtie2 performs local alignment. Very powerful in combination with other tools from the Tuxedo suite such as Tophat

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

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One of the most commonly used mapper. Very efficient and fast. Be carefull however with paired-end reads because Bowtie do not take into account pairs where only one read is properly mapped. I would thus prefer Bowtie2 for paired-end reads. Of note in Bowtie2 : -m option has disappeared... what a pity !