methlab

methlab is a hodgepodge of Python functions to automate various bioinformatics tasks related to bisulphite-converted sequence data. This was written as part of the Epiclines ERC project awarded to Magnus Nordborg at the Gregor Mendel Institute in Vienna. It was designed primarily for internal use and may well make no sense at all to anyone outside the group.

If you do manage to use methlab in your work please cite:

Ellis, T. J., Nizhynska V., Pisupati R., Mollá-Morales A., Nordborg M., (2025), Bisulphite sequencing in the presence of cytosine-conversion errors, PLoS One 20(5):e0322539

Contents

• methlab
• Installation
• Align file names to 96-well plate
• Tools to work with cytosine coverage files
• Disembowel a SAM file
• Discrete methylation states