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genes presence-absence analysis

Hello! I want to identify genes that are present in one genome but missing in other and vice versa. I have already performed annotation (even functional annotation). Please help. Is there software or package(s) do solve this problem? Thank you so much.

pav gene presence-absence
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updated by colindaven colindaven • written by ahmadjoyyia • ahmadjoyyia

1 answer

If they are good quality genomes you can do this quite easily with odgi (after creating a graph with pggb).

See the excellent tutorial here: https://odgi.readthedocs.io/en/latest/rst/tutorials/presence_absence_variants.html

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written by colindaven colindaven

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