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Bowtie

Bowtie

Bowtie is a tool for aligning short DNA sequence reads to a reference genome. The Bowtie algorithm uses the Burrows-Wheeler transform (BWT) technique and permits the use of multiple CPUs.

Topic

Mapping; Bioinformatics; Genomics; Sequencing

Details

  • Operation: Genome indexing; Text mining; Read mapping
  • Input: HTM, FASTA, FASTQ
  • Output: SAM, txt, FASTQ
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Artistic License v2
  • Cost: Free
  • Version name: 1.2.3
  • Maturity: Mature
  • Credit: The National Institutes of Health (NIH)
  • Contact: Ben Langmead langmea _at_ cs.jhu.edu | Cole Trapnell cole _at_ cs.umd.edu | Mihai Pop mpop _at_ umiacs.umd.edu | Steven L Salzberg salzberg _at_ umd.edu
  • Collection: -

Publications

Langmead B, Trapnell C, Pop M, Salzberg SL "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." Genome Biol. 2009;10(3):R25. https://doi.org/10.1186/gb-2009-10-3-r25
PMID: 19261174
PMCID: PMC2690996


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