pycoMeth 0.4.25

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

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Full documentation is available at https://a-slide.github.io/pycoMeth/

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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 calculate the methylation probability at CpG dinucleotide or CpG island resolution across the entire genome and to perform a simple 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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pycoMeth workflow

pycoMeth example output IGV rendering

pycoMeth example HTML report

Example HTML report 1

Example HTML report 2

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Citing

The repository is archived at Zenodo. If you use pycoMeth please cite as follow:

Adrien Leger. (2020, January 28). a-slide/pycoMeth. Zenodo. https://doi.org/10.5281/zenodo.3629254

Authors and contributors

• Adrien Leger (@a-slide) - aleg {at} ebi.ac.uk