PycoMeth

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Version in this branch: 2.2.2

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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.

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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://pmbio.github.io/pycoMeth/

pycoMeth workflow

pycoMeth example HTML report

Example HTML report 1

Example HTML interval report

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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{Snajder2023-wd,
  title    = "pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls",
  author   = "Snajder, Rene and Leger, Adrien and Stegle, Oliver and Bonder, Marc Jan",
  journal  = "Genome Biol.", volume = 24, number = 1, pages = "83", month = apr, year = 2023,
}

Authors

• Rene Snajder (rene.snajder@gmail.com)
• Adrien Leger