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

Detail

  • Operation: Genome indexing;Text mining;Read mapping

  • Software interface: Command-line user interface

  • Language: C++

  • License: Artistic License v2

  • Cost: Free

  • Version name: 1.2.3

  • Credit: The National Institutes of Health (NIH)

  • Input: HTM, FASTA, FASTQ

  • Output: SAM, txt, FASTQ

  • Contact: Ben Langmead langmea@cs.jhu.edu | Cole Trapnell cole@cs.umd.edu | Mihai Pop mpop@umiacs.umd.edu | Steven L Salzberg salzberg@umd.edu

  • Collection: -

  • Maturity: Mature

Publications

  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
  • Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. 2009; 10:R25. doi: 10.1186/gb-2009-10-3-r25
  • https://doi.org/10.1186/gb-2009-10-3-r25
  • PMID: 19261174
  • PMC: PMC2690996

Download and documentation

< Back to DB search