Version in this branch: 2.2.2
DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
pycoMeth can be used for further analyses starting from the output files generated by Nanopolish call-methylation. The package contains a suite of tools to find CpG islands, segment methylome, and to perform a differential methylation analysis across multiple samples.
pycoMeth generates extensive tabulated reports and BED files which can be loaded in a genome browser. In addition, an interactive HTML report of differentially
methylated intervals/islands can also generated at the end of the analysis.
Methplotlib developed by Wouter de coster is an excellent complementary tool to visualise and explore methylation status for specific loci.
Please be aware that pycoMeth is a research package that is still under development. The API, command line interface, and implementation might change without retro-compatibility.
Installation
Install either using conda:
conda install -c snajder-r -c bioconda -c conda-forge pycometh
Or using pip:
pip install pycometh
Documentation
A more detailed usage documentation can be found at https://snajder-r.github.io/pycoMeth/
pycoMeth workflow
pycoMeth example HTML report
Citing
The repository is archived at Zenodo. https://doi.org/10.5281/zenodo.6637645
If you find pycoMeth useful, please cite our preprint:
Snajder, Rene H., Oliver Stegle, and Marc Jan Bonder. 2022. "PycoMeth: A Toolbox for Differential Methylation Testing from Nanopore Methylation Calls." bioRxiv. https://doi.org/10.1101/2022.02.16.480699.
@article {Snajder2022.02.16.480699,
author = {Snajder, Rene and Leger, Adrien and Stegle, Oliver and Bonder, Marc Jan},
title = {pycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls},
year = {2022}, doi = {10.1101/2022.02.16.480699}, publisher = {Cold Spring Harbor Laboratory},
journal = {bioRxiv}
}
Authors
- Rene Snajder (rene.snajder@gmail.com)
- Adrien Leger
Release files for pycoMeth 2.2.2
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