21724594
This reference describes MethylCoder.
| PMID | PMID 21724594 |
|---|---|
| Title | MethylCoder: software pipeline for bisulfite-treated sequences. |
| Year | 2011 |
| Journal | Bioinformatics |
| Author | Pedersen B, Hsieh TF, Ibarra C, Fischer RL. |
| Volume | 17 |
| Start page | 2435 |
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Full text description
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.
