https://github.com/smithlabcode/dnmtools
Tools for analyzing DNA methylation data
https://github.com/smithlabcode/dnmtools
Last synced: 6 months ago
JSON representation
Tools for analyzing DNA methylation data
- Host: GitHub
- URL: https://github.com/smithlabcode/dnmtools
- Owner: smithlabcode
- License: gpl-3.0
- Created: 2022-07-19T21:20:36.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2025-10-17T23:31:31.000Z (6 months ago)
- Last Synced: 2025-10-18T03:45:57.752Z (6 months ago)
- Language: C++
- Homepage: https://dnmtools.readthedocs.io
- Size: 30.6 MB
- Stars: 43
- Watchers: 5
- Forks: 10
- Open Issues: 31
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: code_of_conduct.md
- Maintainers: MAINTAINERS.md
Awesome Lists containing this project
README
[](https://github.com/smithlabcode/dnmtools/releases)
[](https://anaconda.org/bioconda/dnmtools)
[](https://anaconda.org/bioconda/dnmtools)
[](https://anaconda.org/bioconda/dnmtools)
[](https://dnmtools.readthedocs.io/en/latest/?badge=latest)
[](https://www.gnu.org/licenses/gpl-3.0)
DNMTools is a set of tools for analyzing DNA methylation data from
high-throughput sequencing experiments, especially whole genome bisulfite
sequencing (WGBS), but also reduced representation bisulfite sequencing
(RRBS). These tools focus on overcoming the computing challenges imposed by
the scale of genome-wide DNA methylation data, which is usually the early
parts of data analysis.
**Nanopore** As of v1.5.0, DNMTools has funcionality to start analysis with a
BAM file from Nanopore sequencing with 5mC and 5hmC calls at CpG sites.
## Usage
The documentation for DNMTools can be found
[here](https://dnmtools.readthedocs.io).
## Installation
- **Linux**
[binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-Linux.tar.gz).
Should work on any Linux distribution since roughly 2017.
- **Mac**
[binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-macOS.tar.gz).
Should work on any Mac hardware and macOS-13 (Ventura) or newer.
- **Conda**
```console
conda install -c bioconda dnmtools
```
- **Source**
[dnmtools-1.5.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1.tar.gz). Dependencies:
[GSL](http://www.gnu.org/software/gsl),
[HTSlib](https://github.com/samtools/htslib),
[libdeflate](https://github.com/ebiggers/libdeflate) and
[ZLib](https://github.com/madler/zlib). Installing HTSlib as a package
should also give you ZLib and libdeflate. System-specific details below.
Build DNMTools like this:
```console
tar -xf dnmtools-1.5.1.tar.gz
cd dnmtools-1.5.1
./configure --prefix=$HOME
make
make install
```
To get dependencies and a compiler on (these might with OS/package updates):
Ubuntu/Debian
```console
apt-get install build-essential htslib-dev libgsl-dev
```
RedHat/Fedora
```console
dnf install @c-development @development-tools htslib-devel gsl-devel awk
```
Homebrew (see notes below)
```console
brew install gcc htslib gsl
```
Conda (see notes below)
```console
conda create -n build-env -c conda-forge -c bioconda \
gcc gxx make autoconf automake htslib gsl zlib binutils && \
conda activate build-env
```
Notes: If you use only Homebrew or only Conda to setup your environment, you
could need additional dependencies, and some of what I listed you might
already have. You might need to set additional environment variables or run
configure differently. For example with Homebrew:
```console
./configure CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
```
## Contact
Andrew D. Smith
andrewds@usc.edu
## Copyright and License Information
Copyright (C) 2022-2025
Andrew D. Smith and Guilherme de Sena Brandine
Authors of DNMTools: Andrew D. Smith and Guilherme de Sena Brandine
Essential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li, Jenny Qu,
Qiang Song, Fang Fang and Masaru Nakajima
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.