Ultrafast and Memory-Efficient Alignment of Short DNA Sequences to the Human Genome

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.

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).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Base Sequence*
  • Genome, Human / genetics*
  • Humans
  • Sequence Alignment / methods*