What is the best tool to remove redundancy from annotated genome files?

Question

[Monika]

Hi,

I am going to work with annotated wasp genome, but there is a lot of redundancy in the annotation. Meaning there is a lot of different hits for most of the predicted coding regions. The genome was annotated with Maker2. I would like to filter it and keep only the best quality matches. I was wondering if you could propose the best tool for it? Note that this is the first time assembled genome, there is no reference or any other research.

Thank you in advance :)

[GenoMax]

Does this signify that you did not remove sequence redundancy in the contigs what you had assembled before doing the annotation?

[Monika]

I haven't done the assembly by myself. I have a ready gff3 file to work with, but as long as I know, all duplicates were filtered and the assembly has been validated before the annotation.

[lieven.sterck]

You mean redundancy in the functional annotation part? Would it be possible to post a small extract of the gff3 file (indicating the redundancy)?

[Monika]

Here is a screen of one CDS position in gff3