diploid assemblies, how do we annotate?

[nextgenusfs]

Several discussions at Fungal26 --> how should this be done? Can we build an easy button?

[hyphaltip]

I feel like we annotate only one haplotype. generally hifiasm and canu will generate separate haplotype files.
When it comes to depositing these in NCBI we annotate a primary haplotype and then deposit the secondary. I think maybe both use same locus tags but need to check.

[nextgenusfs]

Yeah, agreed. annotate the more complete haplotype, but then would be nice to do a liftover (or targetted re-prediction) to the other haplotype and unify names maybe or at least show relatedness.