Any recommendation for pan-genome annotation?

[lw78943]

Dear Cactus developers,

Thank you so much for sharing this amazing tool with the community. It is very easy to run and fast! I have constructed a graph pan-genome using this pipeline. In the next step, I hope to predict genes in the graph pan-genome and hopefully call the gene present absent variations. Is it possible to do that? I am trying to find resources to do that, but haven't found any useful information. Do you have any suggestions for me? Appreciate your support and help!

Bests,

Li

[glennhickey]

I haven't really used it but odgi pav sounds relevant to this question. Note that cactus-pangenomecan output chromosomal and full-genome odgi files with --chrom-og and --odgi, respectively (and the odgi binary is included in cactus).

[lw78943]

Hi,

Thanks for providing the information. odgi pav can call present/absent variations, but I am more interested in genome annotation. For linear FASTA genome, we can predict genes using MAKER or BRAKER, but I don't know how to do genome annotation for the result of Minigraph-cactus, the graph pangenome. Do you know any software that can predict genes in graph pangenome? Appreciate your support and help!

Have a great day,

Li

[glennhickey]

You can try CAT

[lw78943]

That's great! I will try it. Thanks for sharing. I will close this issue now.