Finished the Pilon prep (except for .sam -> .bam conversion) yesterday afternoon. Found a 32-35% mapping rate for Illumina sequencing files to the PacBio backbone. Not great, but hopefully the whole meta-assembly route will manage to combine everything together in to one super assembly.
For fun, I mapped an Illumina file to a couple of the BGI assemblies, and got ~75% mapping. Wish we could have gotten that out of the PacBio thing, but ah well.
Im transferring the .sam files over to Owl now, but they’re ~40gb a piece, so that’ll take a bit. Will update here when finished!