Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA
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
Genome Biology 2010, 11:R99 doi:10.1186/gb-2010-11-10-r99Published: 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.