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BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.

ABSTRACT: DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.

SUBMITTER: Lim JQ

PROVIDER: S-EPMC3491410 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.

Lim Jing-Quan JQ Tennakoon Chandana C Li Guoliang G Wong Eleanor E Ruan Yijun Y Wei Chia-Lin CL Sung Wing-Kin WK

Genome biology 20121003 10

DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes component ...[more]

PMID: 23034162

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