/ccsmeth

Detecting DNA methylation from PacBio CCS reads

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

ccsmeth

Detecting DNA methylation from PacBio CCS reads

Contents

Installation

ccsmeth is built on Python3 and PyTorch.

install from github (latest version)

git clone https://github.com/PengNi/ccsmeth.git
cd ccsmeth
python setup.py install

Trained models

See models:

  • model_cpg_attbigru2s_hg002_15kb_s2.b21_epoch7.ckpt: a CpG model trained using HG002 PacBio Sequel II (kit 2.0) CCS subreads.

Quick start

Usage

Acknowledgements

  • We thank Tse et al., The Chinese University of Hong Kong (CUHK) Department of Chemical Pathology, for sharing their code and data, as reported in Proc Natl Acad Sci USA 2021; 118(5): e2019768118. We made use of their data and code for evaluation and comparison.
  • We thank Akbari et al., as part of the code for haplotyping were taken from NanoMethPhase of Akbari et al.

License

Copyright (C) 2021 Jianxin Wang, Feng Luo, Peng Ni

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 https://www.gnu.org/licenses/.

Jianxin Wang, Peng Ni, School of Computer Science and Engineering, Central South University, Changsha 410083, China

Feng Luo, School of Computing, Clemson University, Clemson, SC 29634, USA