Homotetraploid, super-large genome, with different parameters, the size of p_utg varies greatly？ about hifiasm HOT 2 OPEN

--n-hap is used to determine the coverage of heterozygous nodes or contigs. For your sample, hifiasm thinks the homozygous coverage is 26, and the heterozygous coverages are 26/2 = 13 and 26/4 = 6 using --n-hap 2 and --n-hap 4, respectively. Hifiasm keeps any node in the assembly graph with coverage above the heterozygous coverage threshold as a real node, instead of sequencing errors. This is why --n-hap 4 leads to a larger graph. Could you please have a try with --hom-cov 55 and --n-hap 2? Since bv looking at the k-mer plot, there are only two peaks and the homozygous coverage should be 55.

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Dear author,
I tried your suggestions, and here are the results:

hifiasm --n-hap 2 -t 120 -l 0 --hom-cov 55 the generated .p_ctg.gfa file is of size 56G, and the .p_utg.gfa file is of size 66G.

Since mine is a homologous tetraploid, which form should I choose for assembly, p_ctg or p_utg?

p_ctg N50: 100MB
p_utg N50: 1MB

I believe that increasing the depth of HiFi data will not increase the length of N50.

For the above question, could you provide some debugging suggestions? Thank you for your valuable time and assistance. I sincerely look forward to your response！

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