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{{Bioinformatics application
|sw summary=The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools for identifying higher-level methylation features, such as hypo-methylated regions (HMR), partially methylated domains (PMD), hyper-methylated regions (HyperMR), and allele-specific methylated regions (AMR).
|bio domain=EpigenomicsEpigenetics, DNA methylation, Bisulfite Sequencing,|bio method=Bisulfite mapping, Analysis Pipeline,|bio tech=Illumina, Illumina HiSeq, Illumina Solexa,
|created by=Song Q et al
|created at=University of Southern California,
== Description ==
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=== List of tools in MethPipe ==={| class="wikitable"|-! 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|-|hmr_plant || identify hyper-methylation in plants and organisms showing mosaic methylation|-|pmd || identify large partially methylated domains|-|amrfinder || identify allele-specific methylated regions |}