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