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Genome Biol. 2010;11(10):R99. doi: 10.1186/gb-2010-11-10-r99. Epub 2010 Oct 8.

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.

Author information

  • 1Department of Computer Science, University of California, Los Angeles, Boelter Hall, Los Angeles, CA 90095, USA. nhomer@cs.ucla.edu

Abstract

A primary component of next-generation sequencing analysis is to align short reads to a reference genome, with each read aligned independently. However, reads that observe the same non-reference DNA sequence are highly correlated and can be used to better model the true variation in the target genome. A novel short-read micro realigner, SRMA, that leverages this correlation to better resolve a consensus of the underlying DNA sequence of the targeted genome is described here.

PMID:
20932289
[PubMed - indexed for MEDLINE]
PMCID:
PMC3218665
Free PMC Article

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