MethPipe: a computational pipeline for analyzing bisulfite sequencing data

The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS).

Quick start


Program Description
rmapbs, rmapbs-pe map bisulfite treated short reads
duplicate-remover remove duplicate reads
methcounts calculate methylation level and read coverage at individual sites
bsrate estimate bisulfite conversion rate
hmr identify hypo-methylated regions
hypermr identify hyper-methylation in plants and organisms showing mosaic methylation
pmd identify large partially methylated domains
amrfinder identify allele-specific methylated regions
roimethstat compute methylation level by genomic region of interest
mlml consistently estimate 5-mC and 5-hmC levels. See MLML homepage.
Table 1: List of tools in the MethPipe package


Workflow for analyzing bisulfite sequencing data (WGBS)

Figure 1: Work flow of the MethPipe package for analyzing bisulfite sequencing dataset


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Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLOS ONE 8(12): e81148 [PDF] [Publisher Site]