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

Nils Homer123* and Stanley F Nelson2

Author Affiliations

1 Department of Computer Science, University of California - Los Angeles, Boelter Hall, Los Angeles, CA 90095, USA

2 Department of Human Genetics, David Geffen School of Medicine, University of California - Los Angeles, 695 Charles Young Drive South, Los Angeles, CA 90025, USA

3 Current address: Ion Torrent, Life Technologies, 7000 Shoreline Court, South San Francisco, CA 94080, USA

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Genome Biology 2010, 11:R99  doi:10.1186/gb-2010-11-10-r99

Published: 8 October 2010


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 re-aligner, SRMA, that leverages this correlation to better resolve a consensus of the underlying DNA sequence of the targeted genome is described here.