https://github.com/smithlabcode/methpipe
A pipeline for analyzing DNA methylation data from bisulfite sequencing.
https://github.com/smithlabcode/methpipe
Last synced: 4 months ago
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A pipeline for analyzing DNA methylation data from bisulfite sequencing.
- Host: GitHub
- URL: https://github.com/smithlabcode/methpipe
- Owner: smithlabcode
- Archived: true
- Created: 2014-04-21T00:12:54.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2022-10-07T20:37:20.000Z (over 3 years ago)
- Last Synced: 2025-04-01T00:29:55.441Z (about 1 year ago)
- Language: C++
- Homepage: http://smithlabresearch.org/methpipe
- Size: 9.29 MB
- Stars: 70
- Watchers: 16
- Forks: 27
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
NOTICE: MethPipe is no longer maintained in this repository
============================================================
MethPipe is now [DNMTools](https://github.com/smithlabcode/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](https://github.com/smithlabcode/dnmtools)
------------------------------------------------------------------
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](https://github.com/smithlabcode/methpipe/releases/tag/v5.0.1),
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](http://www.gnu.org/software/gsl).
* 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](https://github.com/samtools/htslib).
### Configuration
1. Download methpipe-5.0.1.tar.gz [here](https://github.com/smithlabcode/methpipe/releases/download/v5.0.1/methpipe-5.0.1.tar.gz).
2. Unpack the archive:
```
$ tar -zxvf methpipe-5.0.1.tar.gz
```
3. Move into the methpipe directory and create a build directory:
```
$ cd methpipe-5.0.1
$ mkdir build && cd build
```
4. 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
=================================
Copyright (C) 2018-2021
University of Southern California,
Andrew D. Smith
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.