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Generates per-base methylation data given a set of bisulfite-treated reads. MethylCoder provides the option to use either of two existing short-read aligners, each with different strengths. It accounts for soft-masked alignments and overlapping paired-end reads. MethylCoder outputs data in text and binary formats in addition to the final alignment in SAM format, so that common high-throughput sequencing tools can be used on the resulting output. It is more flexible than existing software tool and competitive in terms of speed and memory use.

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MethylCoder classification

MethylCoder specifications

Software type:
Restrictions to use:
Output format:
SAM, tab-delimited text
Programming languages:
C, Python
Computer skills:
Command line interface
Input format:
Operating system:
MIT License

MethylCoder distribution


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MethylCoder support



  • Brent Pedersen <>


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Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA

Funding source(s)

National Institute of Health grant R01-GM069415

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.