HiFi and Nanopore behave differently in 3D DNA (due to different draft assembly sizes)

[Ao Qo]

I have HiFi + HiC, Nanopore + HiC data
The draft assembly of HiFi was finished by Hifiasm, draft assembly of Nanopore was finished by Nextdenova
The first is that the two sequencing methods, the resulting draft assemblies differ by about 600M. (HiFi : 3.1G, Nanopore: 2.5GM)

Based on such draft assembly, the size of the chromosome part finally obtained by HiFi and nanopore is the same (more than 2.4G)

I have 8 genomes, 2 are HiFi and 6 are Nanopore. The results are consistent with the above.
I can now determine that the chromosome size of my species is 2.4~2.5G，because the results for the eight genomes are the same

In the draft assembly, the extra 600M of HiFi is also the part that cannot be anchor on the chromosome. In the heat map, there is no interaction matrix in this part.

I think the extra 600M should be redundant and repetitive

HiFi + HiC    heatmap

Nanopore + HiC     heatmap