MethPipe statistics

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chevron_left Bioinformatics workflows Read alignment Bisulfite conversion rate estimation Methylation scoring Differentially methylated region detection Allele-specific DNA methylation detection chevron_right
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Associated diseases

MethPipe specifications


Unique identifier OMICS_00603
Name MethPipe
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM, SAM
Output format BAM, tab-delimited text
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 3.3.1
Stability Stable
Maintained Yes


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  • person_outline Andrew Smith <>

Publication for MethPipe

MethPipe in publications

PMCID: 5870497
PMID: 29580210
DOI: 10.1186/s12864-018-4594-0

[…] by assessing number of unconverted cytosines that aligned to the lambda genome from the lambda spike-in control and assessment of typically unmethylated cyotsines across the genome using the methpipe software [] (details: additional file : table s5)., cytosines that had an average coverage across all samples of 5 or more reads and displayed at least 10% methylation levels in three […]

PMCID: 5752839
PMID: 29076502
DOI: 10.1038/cr.2017.134

[…] (version: 0.16.3; parameter settings: “bismark --pbat -n 1 -l 40”). potential pcr duplicates were removed using the deduplicate bismark command., post-alignment analysis was performed by using the methpipe package. first, aligned sequences were converted to methpipe format using the to-mr command. methylation levels and coverage for each symmetric cpg site were calculated by the methcounts […]

PMCID: 5655803
PMID: 29065907
DOI: 10.1186/s13059-017-1335-7

[…] at reference cytosine positions in the lambda genome. see below for sequencing and conversion statistics., dna-methylation free (hypo-methylated) regions were detected using the hmr tool from methpipe version 3.0.0 ( [], to consider a region as actively transcribed, we measured the h3k36me3 and rnapii marks (as rpkm) of 200,000 random regions […]

PMCID: 5138066
PMID: 27980397
DOI: 10.4137/BBI.S38427

[…] kernel smoothing (dmr-cate), nonparametric and kernel-based method (m3d), beta-binomial model (methylsig), beta-binomial hierarchical model (moabs), hidden markov model (nhmmfdr), three-state hmm (methpipe), shannon entropy (qdmr), and a binary segmentation algorithm combined with a two-dimensional statistical test (metilene). usually, the latest software compares with some previous methods […]

PMCID: 4896262
DOI: 10.1186/s13167-016-0054-6

[…] setup genome- and immunome-wide biomarker-discovery as well a targeted technologies using multiplexed technologies for validation of these markers. combining the relevant technologies we call these methpipe and peppipe for enabling us streamlined biomarker-development for dna-methylation and antibody-based diagnostics., results interpretation: plasma derived cell free dna methylation maker […]

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MethPipe institution(s)
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA

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