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. 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).

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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.

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