BatMeth is an algorithm that integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes to improve unique mapping rate, speed and precision.
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Genome Biol. 2012 Oct 3;13(10):R82. [Epub ahead of print]
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.