SRMA (Short Read Micro re-Aligner) is a software package that performs sequence re-alignment for next generation sequencing technology.It fixes artifacts introduced by aligning each read independently, significantly reducing the false positive detection, while cleaning insertions and deletions.
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Homer N, Nelson SF.
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA.
Genome Biol. 2010 Oct 8;11(10):R99 PMID: 20932289