Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Dec;9(12):1185-8.
doi: 10.1038/nmeth.2221. Epub 2012 Oct 28.

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

Santiago Marco-Sola  1 , Michael Sammeth, Roderic Guigó, Paolo Ribeca
Affiliations

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

Santiago Marco-Sola et al. Nat Methods. 2012 Dec.

Abstract

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).

PubMed Disclaimer

Comment in

  • GEM: crystal-clear DNA alignment.
    Faust GG, Hall IM. Faust GG, et al. Nat Methods. 2012 Dec;9(12):1159-61. doi: 10.1038/nmeth.2256. Nat Methods. 2012. PMID: 23223169 No abstract available.

References

    1. Nat Methods. 2010 Aug;7(8):576-7 - PubMed
    1. Genome Biol. 2009;10(3):R25 - PubMed
    1. Bioinformatics. 2010 Mar 1;26(5):589-95 - PubMed
    1. Nat Methods. 2011 Dec 18;9(2):176-8 - PubMed
    1. Nat Methods. 2012 Mar 04;9(4):357-9 - PubMed

Publication types