How to filter a reference genome for single copy genes?

Question

[Armin]

Hi everyone,

I've a big genome, 3Gb, I did BUSCO, and found out 10% as duplicated. Given the complexity of the genome I was suggested to take out the single copy genes and basically create a copy of the genome just with single copy genes. I'd appreciate your input on this, what is a correct approach to take?

Cheers,

Armin

[Pierre Lindenbaum]

use bedtools maskfasta ? https://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html