MethylCoder: software pipeline for bisulfite-treated sequences

@article{Pedersen2011MethylCoderSP,
  title={MethylCoder: software pipeline for bisulfite-treated sequences},
  author={Brent Pedersen and Tzung-Fu Hsieh and Christian Ibarra and Robert L. Fischer},
  journal={Bioinformatics},
  year={2011},
  volume={27 17},
  pages={2435-6}
}
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… CONTINUE READING
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