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This article is part of a special issue on epigenomics.

Open Access Method

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation

Jing-Quan Lim1, Chandana Tennakoon12, Guoliang Li3, Eleanor Wong34, Yijun Ruan3, Chia-Lin Wei45 and Wing-Kin Sung13*

Author affiliations

1 Department of Computer Science, National University of Singapore, Singapore 117417

2 NUS Graduate School for Integrative Sciences and Engineering, (CeLS), #05-01, 28 Medical Drive, Singapore 117456

3 Genome Institute of Singapore, 60 Biopolis Street, #02-01 Genome, Singapore 138672

4 Department of Biological Sciences, National University of Singapore, Singapore 117543

5 Joint Genome Institute, Walnut Creek, CA 94598, USA

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Citation and License

Genome Biology 2012, 13:R82  doi:10.1186/gb-2012-13-10-r82

Published: 3 October 2012

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/ webcite.