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

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

http://dx.doi.org/10.1186/gb-2010-11-10-r99
http://www.ncbi.nlm.nih.gov/pubmed/20932289