pycoMeth 0.3.0

Python package for nanopore DNA methylation analysis downstream to Nanopolish

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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. However, this is not a visualisation tool per se. An excellent complementary tool to visualise and explore methylation status for specific loci is Methplotlib developed by Wouter de coster.

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

Authors

• Adrien Leger - aleg {at} ebi.ac.uk