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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. © 2010 Homer and Nelson; licensee BioMed Central Ltd.
Homer, N., & Nelson, S. F. (2010). Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biology, 11(10). https://doi.org/10.1186/gb-2010-11-10-r99