NOTICE: MethPipe is no longer maintained in this repository

MethPipe is now DNMTools. The MethPipe repository will remain open for issues and discussion, but further releases, updates and fixes will no longer be maintained in this page. We strongly recommend that users replace their existing release of MethPipe with the most recent version of DNMTools, which contains all existing MethPipe programs along with various fixes, improvements and novel programs for bisulfite sequencing data analysis.

Visit the DNMTools repository

The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (WGBS and RRBS). MethPipe provides tools methylation-specific technical evaluation of sequencing data, and for estimating methylation levels at individual cytosines. 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).

Release 5.0.1

This new release no longer supports mr files, which means that the to-mr program has been eliminated and replaced by a program called format_reads, which merges mates in paired-end SAM files, also converting them to a standardized SAM format depending on the mapper it originates from. Additionally, the htslib library is now required, and instructions to install it in different environments are discussed below.

If working with MR files is necessary for your analysis, we refer users to methpipe version 5.0.1, which is the last release that contains programs that take MR as input.

Installing release 5.0.1

Required libraries

A recent compiler: most users will be building and installing this software with GCC. We require a compiler that fully supports C++11, so we recommend using at least GCC 5.8. There are still many systems that install a very old version of GCC by default, so if you have problems with building this software, that might be the first thing to check.
The GNU Scientific Library: this has always been required. It can be installed using apt on Linux, using brew on macOS, or from source available here.
The Zlib compression library. Most likely you already have this installed on your system. If not, it can be installed using apt on Linux through the package zlib1g-dev. On macOS, Zlib can be installed with brew.
The HTSlib library, which can be installed through brew on macOS, through apt on Linux, or from source downloadable here.

Configuration

Download methpipe-5.0.1.tar.gz here.
Unpack the archive:
```
$ tar -zxvf methpipe-5.0.1.tar.gz
```
Move into the methpipe directory and create a build directory:
```
$ cd methpipe-5.0.1
$ mkdir build && cd build
```
Run the configuration script:
```
$ ../configure
```
If you do not want to install the methpipe system-wide, or if you do not have admin privileges, specify a prefix directory:
```
$ ../configure --prefix=/some/reasonable/place
```
If you installed HTSlib yourself in some non-standard directory, you must specify the location like this:
```
$ ../configure CPPFLAGS='-I /path/to/htslib/headers' \
            LDFLAGS='-L/path/to/htslib/lib'
```

Building and installing the tools

If you are still in the build directory, run make to compile the tools, and then make install to install them. If your HTSlib is not installed system-wide, then you might need to udpate your library path:

$ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib

Building and installing from source

We strongly recommend using methpipe through the latest stable release under the releases section on GitHub. However, developers who wish to work on the latest commits, which are potentially unstable, can compile the cloned repository using the Makefile available in the repository. If HTSLib is available system-wide, compile by running

make

Usage

Read methpipe-manual.pdf in the docs directory.

Contacts and bug reports

Andrew D. Smith andrewds@usc.edu

Ben Decato decato@usc.edu

Meng Zhou mengzhou@usc.edu

MethPipe and MethBase Users’ Mailinglist methpipe@googlegroups.com http://groups.google.com/group/methpipe

Copyright and License Information

Current Authors: Andrew D. Smith, Ben Decato, Meng Zhou, Liz Ji, Terence Li, Guilherme de Sena Brandine

This 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 software 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.