Difference between revisions of "Methpipe"
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{{Bioinformatics application | {{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). | |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=Epigenomics, DNA methylation, Bisulfite Sequencing, | |
| − | |bio domain=Epigenomics, DNA methylation, Bisulfite Sequencing, | + | |bio method=Bisulfite mapping, Analysis Pipeline, |
| − | |bio method=Bisulfite mapping, Analysis Pipeline, | + | |bio tech=Illumina, |
| − | |bio tech=Illumina, | ||
|created by=Qiang Song, et al | |created by=Qiang Song, et al | ||
| − | |created at=University of Southern California, | + | |created at=University of Southern California, |
|maintained=Yes | |maintained=Yes | ||
|email address=methpipe@googlegroups.com | |email address=methpipe@googlegroups.com | ||
| − | |input format=FASTQ, SAM/BAM, | + | |input format=FASTQ, SAM/BAM, |
|language=C++ | |language=C++ | ||
| − | |licence=GPL (>= 3), | + | |licence=GPL (>= 3), |
| − | |os=Linux, Mac OS X, | + | |os=Linux, Mac OS X, |
}} | }} | ||
== Description == | == Description == | ||
Revision as of 21:43, 11 September 2013
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Application data |
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| Created by | Qiang Song, et al |
|---|---|
| Biological application domain(s) | Epigenomics, DNA methylation, Bisulfite Sequencing |
| Principal bioinformatics method(s) | Bisulfite mapping, Analysis Pipeline |
| Technology | Illumina |
| 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
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
To add a reference for Methpipe, enter the PubMed ID in the field below and click 'Add'.
[ edit box ]
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