larger assembly size than kmer estimation genome size about hifiasm HOT 2 OPEN

Why do you need to adjust the assembly size? The output from GenomeScope is an estimate, and not the ground truth. It is better to evaluate the assemblies with such tools as BUSCO and Merqury. If you then see you are missing a lot of data (but you have the opposite case in a way), then you can try different measures.

In short, it is likely fine.

from hifiasm.

Thanks for your suggestions @olekto . I assembled the scaffolds from hifiasm to super-scaffolds with HiC data by 3d-DNA, the depth of HiC data is around ~100X. It resulted in ~310Mb super-scaffold sequences (9 chromosomes of this species), ~60-90 Mb fragment sequences. I thought the fragment sequences are too many, therefore I want to adjust the assembly size.

By the way, what the fragment sequences usually are? Do the T2T genomes have no fragment sequences when assembled with HiC data?

Thanks.

from hifiasm.