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

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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