How to combine or reconcile genome annotation using different methods?

Question

[margiezilla]

Hi all,

We're running an annotation pipeline on a novel eukaryotic genome using funannotate (wrapper script that performs gene prediction with Augustus, snap, GlimmerHMM, etc), both alone just using RNA-seq data and also feeding it protein sequences from 2 different but related species. I'm wondering if there is a good method to reconcile / combine these annotations into some kind of consensus? The underlying method that funannotate uses is EvidenceModeler, I wonder if that could be used again to get another weighted consensus annotation. Thanks again! Relatively new to genome annnotation here.

M