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human-pangenomics / hpp_pangenome_resources

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Why not choose vg to construct pan genome？ #2

Closed zhoudreames closed 2 years ago

zhoudreames commented 2 years ago

I'm very curious about why I can't adapt to vg to construct pangenome Is there any limitation in vg method? we used hifi data to obtain multiple haplotype-revolved assemblies，but I don't know how to choose which method to construct the pangenome？ Is there any recommendation ？ thanks~

glennhickey commented 2 years ago

Sorry, I only noticed this issue now while doing something else. This is a good question, and you're probably best looking at the paper https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1.abstract for a discussion on it.

with vg construct graphs are created from reads -> map-against-reference -> variant calls -> VCF -> graph whereas the graphs presented here are created from reads->assembled genome-> multiple genome alignment -> graph by using the multiple alignment, we hope to have better representation of complex variation, particularly in regions that are not easily represented along the reference.

zhoudreames commented 2 years ago

thanks~