MethylCoder: software pipeline for bisulfite-treated sequences |
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Authors: | Pedersen Brent Hsieh Tzung-Fu Ibarra Christian Fischer Robert L |
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Institution: | Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. bpederse@gmail.com |
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Abstract: | MOTIVATION: MethylCoder is a software program that generates per-base methylation data given a set of bisulfite-treated reads. It 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 and competitive in terms of speed and memory use. AVAILABILITY: MethylCoder requires only a python interpreter and a C compiler to run. Extensive documentation and the full source code are available under the MIT license at: https://github.com/brentp/methylcode. CONTACT: bpederse@gmail.com. |
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