I have acquired genomic reads from nanopore and pacbio technologies for a diatom lacking a reference sequence.
I want to build a good reference assembly and would like to incorporate both nanopore and pacbio reads in the same run.
If this is not possible, is there a way to get a consensus assembly from 2 separate assemblies?
Bonus: I also have A LOT of RNA-seq data for this diatom. Is it possible to use this to "polish" the genomic scaffolds? I know polishing is usually using shotgun genomics but I'm wondering if there is a way to use these RNA-seq datasets in the same way? I don't expect there to be many introns but there are some...this may make it difficult/impossible to reliably use RNA-seq data.