Full documentation is available at https://a-slide.github.io/pycoMeth/
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.
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
- Adrien Leger (@a-slide) - aleg {at} ebi.ac.uk