I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, Duplications, Inverted regions in my Query sequence on the Y-axis (PacBio Hifi) compared to the reference genome.
I want to check if these structural variations are real or only resulting from sequencing errors or not. So, I want to manually curate the PacBio assembly. Because I can see at which contig the structural variations are.
Can you please suggest any tools for manual curation of a genome assembly to investigate whether these structural variations are sequencing errors or real sequence variation?