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.

Installation

• Linux binary. Should work on any Linux distribution since roughly 2017.

• Mac binary. Should work on any Mac hardware and macOS-13 (Ventura) or newer.

• Conda

  conda install -c bioconda dnmtools

• Source dnmtools-1.5.1.tar.gz. Dependencies: GSL, HTSlib, libdeflate and ZLib. Installing HTSlib as a package should also give you ZLib and libdeflate. System-specific details below.

  Build DNMTools like this:

  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

  apt-get install build-essential htslib-dev libgsl-dev

  RedHat/Fedora

  dnf install @c-development @development-tools htslib-devel gsl-devel awk

  Homebrew (see notes below)

  brew install gcc htslib gsl

  Conda (see notes below)

  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:

  ./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.