Methpipe
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Application data |
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| Created by | Song Q et al |
|---|---|
| Biological application domain(s) | Epigenetics, DNA methylation, Sequencing |
| Principal bioinformatics method(s) | Bisulfite mapping |
| Technology | Illumina, Illumina HiSeq, Illumina Solexa |
| Created at | University of Southern California |
| Maintained? | Yes |
| Input format(s) | FASTQ, SAM/BAM |
| Programming language(s) | C++ |
| Licence | GPL (>= 3) |
| Operating system(s) | Linux, Mac OS X |
| Contact: | methpipe@googlegroups.com |
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).
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Description
List of tools in MethPipe
| 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 |
Links
- Methpipe Homepage [ edit link ]
- Methpipe Mailing list [ edit link ]
- Methpipe Manual [ edit link ]
- Methpipe Related [ edit link ]
- Methpipe Related [ edit link ]
- Methpipe Source code [ edit link ]
References
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