Run purge dups on a nanopore hifi hybrid assembly

[ericgonzalezs]

Hi,

I have a Hifiasm assembly generated from HiFi + Nanopore data. I’m wondering what is the best approach is to run purge_dups. Should I align the Nanopore reads or the HiFi reads? I’m concerned that the reads might cover different parts of the assembly.

I was thinking that Nanopore reads might provide broader coverage (though less accurate), while HiFi read alignments could be more precise. Any suggestions on this would be greatly appreciated.

Thanks