larger assembly size than kmer estimation genome size

[leon945945]

Hi, I estimated the genome size with HiFi data, the estimated genome size is 328Mb with 1.02% hetorozygosity:

I assembled the primary genome and phased genome with HiC data by hifiasm. The size of primary genome is 409Mb and two phased haplotype are 389Mb and 366Mb with default hifiasm -s 0.55. They are larger than the estimation genome size.

Then I adjusted the parameter to -s 0.3, the primary genome size decreased to 396Mb, two phased haplotype size decreased to 377Mb and 356Mb. They are still larger than the estimation size.

Could you please give me some suggestions on how to adjust the assembly size. Thanks.

[olekto]

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.

[leon945945]

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.