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Published 20 hours ago • verified publisher icon chhylp123

Using hifiasm for triploid phasing assembling, --n-hap 3 doesn't work

Open liuxin-21d opened this issue 1 year ago • 2 comments

Hi, Thanks for your nice hifiasm. I was using hifiasm to assemble triploid recently, and i used --n-hap 3, but i just got hap1 and hap2 without hap3. It seems that hifiasm works not very well with triploid phasing assembling? Or should i configure other special parameters for triploid phasing assembling? Looking forward to your reply. Best regards, Liu Xin

liuxin-21d avatar Oct 11 '22 08:10 liuxin-21d

No, hifiasm cannot output 3 haplotypes right now in default. If you would like to get phased assemblies for triploid samples, you need additional phasing information like the genetic map. Here is a nice example: https://github.com/baozg/Potato_C88.

chhylp123 avatar Oct 12 '22 21:10 chhylp123

i will try it then. Thank you for your reply and suggestion.

liuxin-21d avatar Oct 13 '22 02:10 liuxin-21d