Why use Hi-C and/or Bionano for scaffolding when Nanopore sequencing exists?

Question

[Mark]

This might be a very naive question but I'm still relatively new to the genomics field.

I'm reading a lot about high quality genome reconstructions and I notice a lot of modern assemblies rely on scaffolding PacBio Hifi-assembled contigs to HiC or Bionano data. I'm wondering, why bother with that when Nanopore sequencing can give you extremely long reads? From what I can tell, all scaffolding techniques require HMW DNA to work, and a Nanopore sequencing prep isn't very cumbersome unlike what I can tell from the HiC and Bionano library preps. Even if the Nanopore reads aren't totally accurate, they should be accurate enough to resolve gaps and assemble scaffolds no? I don't really see the rationale behind using HiC or Bionano it seems needlessly tedious. I feel like I'm missing something. Can anyone help me understand why this is still the standard approach?

[alex.zaccaron]

There are many organisms that are difficult to get high-quality HMW DNA. After sequencing (assuming it works, because sometimes DNA has unknown properties that kills the pores), the resulting nanopore reads might not be good enough to resolve repetitive regions, and the assembly is fragmented. Scaffolding with Hi-C can be helpful in these and other situations.

Answer 1

[shelkmike]

The main reason is that repeat clusters can be very long. This is often the case with rDNA repeat clusters and centromeric repeat clusters. Nanopore reads may be not long enough to assemble such regions.