Work with hifiasm using haplotype-specific data

[chenzixi07]

Hello @zengxiaofei , I used hifiasm with hifi and HiC data, and generate haplotype-specific data, including p_ctg.fa, p_utg.fa, r_utg.fa, and hap*.p_ctg.fa. As you mentioned in the tutorial, if I want to run the script below:

/path/to/HapHiC/haphic pipeline allhaps.fa HiC.filtered.bam nchrs --gfa "hap1.p_ctg.gfa,hap2.p_ctg.gfa"

1) Which fa file should I use as the <allhaps.fa>? p_utg, p_ctg, or cat the hap*.p_ctg.fa as one file? According to the previous post #16 , maybe I should cat the hap*.p_ctg.fa as one file?

2) Which fa should I use for HiC reads mapping to generate the <HiC.filtered.bam>?

3) I tested both 46 and 46*3 for scaffolding as I mentioned here #19. I used p_utg.fa as the only input, without hap*.gfa. I am a beginner in genome assembly. It seems that 46 is better for resolving the triploid genome? But the survey of my species seems to be 2n=3x=2.4G, so the size of 46*3 result seems better? I am really confused.

The pic below using the command: haphic pipeline p_utg.fa HiC.filtered.bam 138 --gfa p_utg.gfa

The pic below using the command: haphic pipeline p_utg.fa HiC.filtered.bam 46 --gfa p_utg.gfa

Regards, Zixi