Thanks for your response. Yes, I have a draft genome that was assembled using only PacBio reads, using hifiasm. I also have short reads, but they are not from the same individual as the PacBio reads. I have no other genomic data. The current assembly is ~250Mb, N50 is about 2Mb, and has 350 contigs/scaffolds after testing out several scaffolding tools.
I posted this question because the docs for long read scaffolding tools all mention scaffolding short read assemblies with long reads, so I wasn't sure if scaffolding a long read assembly with long reads was appropriate. (newbie here)
The assembly would ideally be complete and contiguous enough to look at regulatory regions of certain sets of genes.