3d-dna pipeline to scaffolding a hifiasm heterozygous assembly

[ericgonzalezs]

Hi,

I have a haplotype resolved assembly done with hifiasm (HI-C) and Hifi data for a plant genome. I would like to use the 3d-DNA pipeline for the scaffolding and produce a haplotype-resolved final assembly. I am wondering if you could please advise me on the best way to achieve this. One possibility could be to run each haplotype assembly separately and then use the Hi-C data of the heterozygous individual twice, on each assembly, with the haploid mode. But I am not sure if it is a good idea to use the heterozygous Hi-C data on each assembly. Another option could be to run the two haplotype assemblies toguetter, but I am not sure how the 3d-dna pipeline could work on this and if to run it like this I have to use the diploid mode. I am also not sure if I should use the juicer diploid mode too. I´ll really appreciate any idea or suggestion.

[Lichuncai]

I have the same question, can somebody please help out? Thanks!

[acboulet]

Interested the above question as well. Any success finding an answer?