MethylCoder

MethylCoder is a software program designed to generate per-base methylation data from a set of bisulfite-treated reads. It supports two short-read aligners, accounts for soft-masked alignments and overlapping paired-end reads, and outputs data in text, binary, and SAM formats for compatibility with common high-throughput sequencing tools. MethylCoder is flexible, fast, and requires only a python interpreter and a C compiler to run.