Pangenome validation

Question

[aaaniich]

Hey, everybody! I'm diving into the topic of pangenome. My team and I have already collected many different variations of the pangenome graph, but I'd like to clarify a couple details. Is there any reliable way how to validate the pangenome graph for adequacy? Maybe pull out some individual complex regions to check or some quality metrics. I'd be happy to have any help.

[Uveyik]

Hi, as far as I know, odgi and vg has validation functionality. odgi validate accepts .og and gfav1 files, validates the graph checking if the paths are consistent with the graph topology. vg validate can be used for verification of a gam file.