Skip to main content

Differential methylation calling suite for Nanopore methylation calls PycoMeth

Project description


GitHub license Language DOI

PyPI version PyPI downloads Anaconda Version Anaconda Downloads

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.


Install either using conda:

conda install -c snajder-r -c bioconda -c conda-forge pycometh

Or using pip:

pip install pycometh


A more detailed usage documentation can be found at

pycoMeth workflow


pycoMeth example HTML report

Example HTML report 1

Example HTML report 2


The repository is archived at Zenodo.

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.

@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}


Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pycoMeth-2.2.2.tar.gz (51.8 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page