Create a GenBank file for a novel organism

Question

[scarface]

I have assembled a novel genome. I have diamond blast (against swissprot, nr), and interproscan annotation result files. How to combine these to make a genbank file? I also want to use the genbank for reconstruction of pathways in EcoCyc.

Please note the organism I am working with is an eukaryote (a hemipteran insect).

[Joe]

GenBank has been kinda superceded by GFF3 formats - is it a genbank you need specifically?

I would suggest just using an annotation pipeline which should spit that data out. Eukaryotes is not my experience, but in the microbial world we have tools like prokka which interfaces many tools. I am sure there must be an equivalent for Euk work

[scarface]

Prokka is useful as a one step annotation tool for prokaryotes. Unfortunately for eukaryotes, I could not find any such annotation engine. Closest one I have come across is Funannotate, but I am unable to parse the braker3 results for Funannotate functional annotation. Therefore, I decided to run EggNOG-mapper, Interproscan, and Blast myself. But combining all this information is something I am still unable to figure out.

GFF3 is a good idea, but the emapper GFF3 output is horrible and needs reformatting. Looking for anybody who has countered these issues before...

Thanks

[scarface]

Btw, if someone is still looking for the answer, you can use funannotate annotate command and parse the interproscan xml with the augustus prediction gff3.