Applications/Bowtie1

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Application Details

  • Description: Bowtie is an ultrafast, memory-efficient short read aligner. It 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).
  • Version: 1.1.2
  • Modules: bowtie/1.1.2
  • Licence: Open source (Github)

Usage Examples

Bowtie is an ultrafast, memory-efficient short read aligner. It 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


It provides the following tools:

  • bowtie
  • bowtie-align-l
  • bowtie-align-l-debug
  • bowtie-align-s
  • bowtie-align-s-debug
  • bowtie-build
  • bowtie-buildc
  • bowtie-build-l
  • bowtie-build-l-debug
  • bowtie-build-s
  • bowtie-build-s-debug
  • bowtie-inspect
  • bowtie-inspect-l
  • bowtie-inspect-l-debug
  • bowtie-inspect-s
  • bowtie-inspect-s-debug


With linkages to the following modules too:



[username@login01 ~]$ module load bowtie1/1.1.21

Further Information


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