MethylCoder: software pipeline for bisulfite-treated sequences. 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.
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References in zbMATH (referenced in 2 articles )
Showing results 1 to 2 of 2.
- Barturen, Guillermo; Oliver, José L.; Hackenberg, Michael: Error correction in methylation profiling from NGS bisulfite protocols (2017)
- Sun, Shuying; Yu, Xiaoqing: HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test (2016)