I am currently assembling a teleost genome using HiFi reads and I decided to use Inspector to correct my primary assembly. I observed marked improvements in the assembly after just a single round, but the corrected assembly was not free from errors (see table below). I was wondering if there is any benefit to running inspector in multiple rounds similar to how older long read genomes needed several rounds of polishing? Is there a risk of over-polishing or introducing errors?
I am currently assembling a teleost genome using HiFi reads and I decided to use Inspector to correct my primary assembly. I observed marked improvements in the assembly after just a single round, but the corrected assembly was not free from errors (see table below). I was wondering if there is any benefit to running inspector in multiple rounds similar to how older long read genomes needed several rounds of polishing? Is there a risk of over-polishing or introducing errors?