The GEM mapper: fast, accurate and versatile alignment by filtration

Nat Methods. 2012 Dec;9(12):1185-8. doi: 10.1038/nmeth.2221. Epub 2012 Oct 28.


Because of ever-increasing throughput requirements of sequencing data, most existing short-read aligners have been designed to focus on speed at the expense of accuracy. The Genome Multitool (GEM) mapper can leverage string matching by filtration to search the alignment space more efficiently, simultaneously delivering precision (performing fully tunable exhaustive searches that return all existing matches, including gapped ones) and speed (being several times faster than comparable state-of-the-art tools).

Publication types

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

MeSH terms

  • Algorithms
  • Base Sequence
  • Computational Biology / methods
  • Genome
  • Genomics / methods
  • Humans
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software