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  • How to manually curate a specific region in a genome assembly?

    Hello,

    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 at a specific contig. 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?

    I have uploaded the dot-plot below. Thank you.

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