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An efficient and accurate general-purpose bisulfite sequence mapping program. BatMeth can be deployed for the analysis of genome-wide bisulfite sequencing using either base reads or color reads. It allows asymmetric bisulfite conversion to be detected by labeling the corresponding reference genome with the hit. It 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.

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BatMeth classification

BatMeth specifications

Software type:
Restrictions to use:
Output format:
Custom text format, PDF
Programming languages:
C, C++
Computer skills:
Command line interface
Input format:
Operating system:
MIT License

BatMeth distribution


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BatMeth support



  • Wing Kin Sung <>


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Department of Computer Science, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, (CeLS), Singapore; Genome Institute of Singapore, Genome, Singapore; Department of Biological Sciences, National University of Singapore, Singapore; Joint Genome Institute, Walnut Creek, CA, USA

Link to literature

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