pycoMeth
Welcome to pycoMeth documentation
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 (CGIs)
- create a multi-sample consensus methylome segmentation
- test regions (like CGIs or segments) for differential methylation
- generate interactive HTML report for differentially methylated regions
Since pycoMeth version 2, input files need to be in MetH5 format since this format allows for high performance and parallized access to genomic regions.
Installation
You can install the latest version either via pip
pip install pycoMeth
or via conda
conda install -c snajder-r -c bioconda -c conda-forge pycometh
Usage
The pycoMeth package contains the following modules:
- CGI_Finder: find CpG islands in a fasta file by using a sliding window and merging overlapping windows satisfying the CpG island definition.
- Meth_Seg: Bayesian methylome segmentation algorithm
- Meth_Comp: compare Methylation level between several samples
- Comp_Report: generate an interactive HTML report for top significant differentially methylated intervals
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.
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.
pycoMeth workflow
pycoMeth example HTML report
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