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I would like to gap-fill (or correct) a mammalian-sized assembly for which we have BACs that have been sequenced with PacBio CLR data. I have seen there are pbm22/gcpp tools available for correcting assemblies, but looking at how they've been used, they seem to correct existing assemblies built with FALCON or similar.

Can pbmm2 and gcpp be used with a reference constructed without pacbio data? E.g. given a mammalian-sized reference and a .bam file of PacBio reads for a BAC, what's the best way to gap-fill the current reference? Thx

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My understanding is that PBJelly is the tool intended to solve this problem.

This person seems to have used it starting with Illumina scaffolds. I have not personally used it but have heard that it works pretty well.

Edit: note that the PacBio ecosystem is not super easy to use from scratch. However, they have made pretty good efforts to facilitate setup using conda, as for instance documented here. This person shows a conda recipe for pbjelly.

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