genes presence-absence analysis

Question

[ahmadjoyyia]

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.

Answer 1

[colindaven]

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