Hello, I have two genome assemblies of a single species generated from Pacbio sequencing and Oxford Nanopore Technology. None of them are chromosome-scale assemblies. The genome size is approximately 1 Gb. The species is a wild species and highly heterozygous. When I compare the two assemblies against different reference genomes from cultivated species, I see lots of inversions and INDELs compared to the reference genomes. This is expected as the reference genome is developed from inbreeding species with much less heterozygosity. But the magnitude of the inversions and INDELs in the two assemblies of the wild species varies quite a lot. Please see the figures.
My questions are: How can I estimate the size and the number of these structural variations in both assemblies?
Is it possible to evaluate if those structural variations are real or sequencing errors?
Is it possible to use the Pacbio assembly to correct and polish the ONT assembly and vice-versa?
I have seen RagTag and SLR for reference guided scaffolding but not sure if I can apply it here. Please provide some suggestions as I plan to develop a high-quality reference genome from these two assemblies.
