A pipeline for analyzing DNA methylation data from bisulfite sequencing.
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The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe also 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).

Building and Installing

You may download the latest stable release from http://smithlabresearch.org/software/methpipe/
This software package has been designed to operate in a UNIX-like environment. It has been tested on MacOS X Snow Leopard and Linux.

  • Step 0

    This software package requires a functioning installation of the GNU Scientific Library (GSL). If you don't already have this installed, you will need to download and install it from http://www.gnu.org/software/gsl/

    If gsl is not installed in the default path,

    export CPATH=/path_to_my_gsl/include
    export LIBRARY_PATH=/path_to_my_gsl/lib

    will add search paths for compiling and linking.

  • Step 1

    To build the binaries, type the following, where '>' is your prompt and the CWD is the root of the distribution:

    > make all
  • Step 2

    To install the binaries, type the following, where '>' is your prompt and the CWD is the root of the distribution:

    > make install

    This will place the binaries in the bin directory under the package root. They can be used directly from there without any additional steps. You can add that directory to your PATH environment variable to avoid having to specify their full paths, or you can copy the binaries to another directory of your choice in your PATH

For advanced users who are interested in the newest features, you may obtain the latest source code by cloning the MethPipe repository:

> git clone --recursive https://github.com/smithlabcode/methpipe.git

After you clone the latest source code, follow the above steps for installation.


Read methpipe-manual.pdf in the docs directory.

Contacts and bug reports

Andrew D. Smith andrewds@usc.edu

Ben Decato decato@usc.edu

MethPipe and MethBase Users' Mailinglist methpipe@googlegroups.com http://groups.google.com/group/methpipe?hl=en

Copyright and License Information

Copyright (C) 2018-2020 University of Southern California, Andrew D. Smith

Current Authors: Andrew D. Smith, Ben Decato, Meng Zhou, Liz Ji, Jenny Qu, Egor Dolzhenko

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

SamTools Copyright (c) 2008-2009 Genome Research Ltd. SamTools software is free software distributed under the MIT License. Refer to the COPYING file in src/samtoos/ for further information.