I have a Unicycler assembly of a bacterial genome from PacBio and Illumina reads. It's a rather small but repetitive genome, and it's didn't assemble into one circualr chromosome, despite having 500x long read coverage.
I've tried few other options (i.e. long read-only assemblers) and they didn't produce a finished genome as well.
I've read that it's possible to finish the assembly by inspecting it with Bandage and by aligning reads to it. However it's not obvious how to do it and what with? Bandage offers BLAST functionality, but I don't think I can blast 500x of PacBio reads onto the graph. Would it make sense to get consensus set of well-corrected reads with Racon? And how does one identify a subset of long reads that potentially span the contig ends?
Thank you for any suggestions.