HiC-Pro non-model species

Hi: I am studying a non-model diploid mammal species with a large genome size (~6GB). I have 30X Hifi data, as well as Hi-C data from Dovetail Genomics using their Chicago libraries. I have made an assembly in HiFiASM with the HiFi data. I would like to use EndHiC to scaffold my assembly with Hi-C data. EndHiC recommends using Hi-C Pro to generate input files. Hi-C Pro wants a table file of chromosome sizes. I don't have chromosome size information for my species. Do you know if I can create a table of scaffold lengths from my HiFiasm assembly? Or do these methods only really work on species with already known genome information? Thanks in advance. best, Andreas

Mar 21 '23 15:03 andreaschavez

Did you find a solution to this? I'm struggling to understand the documentation on this.

Thanks!

Jul 07 '23 13:07 SwiftSeal

Hi SwiftSeal: I'm having similar struggles and haven't proceeded any further. I'm still interested in using the program if it seems feasible.

Jul 07 '23 15:07 andreaschavez

Yeah the config confused me a lot! In the end I just opted for yahs and manual correction with juicertools - had the issue of telomere fusions with yahs but not too tricky to correct manually.

Jul 17 '23 12:07 SwiftSeal