Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop, Steven L. Salzberg

Research output: Contribution to journalArticle

Abstract

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source http://bowtie.cbcb.umd.edu.

Original languageEnglish (US)
Article numberR25
JournalGenome biology
Volume10
Issue number3
DOIs
StatePublished - Mar 4 2009

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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