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Alternative name: Bowtie2

A short read aligner that aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

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4 user reviews

4 user reviews

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

Arup Ghosh

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

Great read mapper.

Claudia Armenise Quartz Bio's avatar image

Claudia Armenise Quartz Bio

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

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 !

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Bowtie classification

Bowtie specifications

Software type:
Restrictions to use:
Computer skills:
Command line interface
Operating system:


  • bowtie-build
  • bowtie-inspect
  • bowtie

Bowtie distribution


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Bowtie support



  • Ben Langmead <>


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Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, MD, USA

Link to literature

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