bicycle: bisulfite-based methylcytosine caller

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH).