Why more contigs always present in haplotype 1 than haplotype 2?

[Lin Cheng]

Hi, I found that the contig number of haplotype 1 from hifiasm are always large contig number of haplotype 2.

What causes this? Is there any explanation in the article （https://www.nature.com/articles/s41587-022-01261-x）?

[chhylp123]

Sorry for the late reply. I feel like in most cases, hifiasm may put unphased contigs to hap1, making hap1 has more small contigs.

[Lin Cheng]

Thanks for your explanations!