result for polyploid

[zhidaobuzhidao]

Hello, I have assembled a tetraploid genome using hifiasm. The size of *r_utg.gfa and *p_utg.gfa are consistent with all tetraploid genome size . *bp.p_ctg.gfa is a little smaller than all tetraploid genome size. When I added "-l 2 -s 0.1 --n-hap 4" ,*bp.hap1.p_ctg.gfa and *bp.hap2.p_ctg.gfa are a little smaller than all tetraploid genome size. Now,I want to know which result should I use for next step ? Could you please give me some surggestions ?

Bests.

[chhylp123]

Which types of assemblies do you want to get, primary assembly or phased assembly?

[zhidaobuzhidao]

I want to get whole information about the polyploid so I concern about the assembly size. Next step I will use HIC data by ALLHic to scaffold this genome to chromosome level . I don't know whether I should use primary assembly or phased assembly. *r_utg.gfa and *p_utg.gfa have a large number of contigs. Can I use *bp.p_ctg.gfa together with *bp.a_ctg.gfa ? Thanks a lot!

[chhylp123]

I'm not familiar with AllHiC, but I guess AllHiC needs p_utg.gfa to keep all information.

[zhidaobuzhidao]

Thanks a lot.

Because the p_utg.gfa's contigs number are large (about 60,000 ) , it is too difficullt to use Juicebox for following analysis. Is it possible that the result of Hic phasing will be userful for me ？Phasing result may be more continuous I think.

[chhylp123]

Yes, but current hifiasm phasing has the diploid assumption. We have some preliminary results on polyploid samples but making it really works takes time.