Fast Gapped-Read Alignment With Bowtie 2

Nat Methods. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.

Abstract

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Databases, Genetic
  • Genome, Human / genetics
  • Humans
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods