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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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Add/remove one assembly (or more) from a pangenome graph #279

Closed LiaOb21 closed 1 year ago

LiaOb21 commented 1 year ago

Dear developers,

I was wondering if there is a way to add or remove assemblies to an already built pangenome graph using pggb. I had a look to the documentation but I couldn't find anything. Sorry if I missed something and thank you in advance!

Lia

subwaystation commented 1 year ago

Dear @LiaOb21,

if you want to remove paths from the graph, please take a look at https://odgi.readthedocs.io/en/latest/rst/commands/odgi_extract.html. -p, --paths-to-extract=FILE should be your friend.

If you want to add assemblies you could theoretically map against the graph using https://github.com/maickrau/GraphAligner. I think with vg augment or vg inject you can embed the mappings in the graph. However, we do not recommend this. If you want to add assemblies, please build the graph again from scratch. This is the most precise way to do it.

LiaOb21 commented 1 year ago

Hi @subwaystation,

Thank you so much for your suggestions. Best regards,

Lia