Let's say one has scaffolded a draft genome with PacBio subreads and PB Jelly, but still is concerned about not enough coverage of Illumina contigs, and the maintenance of PacBio indel errors in the final draft.
This person also have high quality RNA-seq illumina and can map this to the draft genome. One could use a SNP caller to, instead of calling SNPs, to evaluate errors in the draft genome?
Taking into consideration the species for which the draft genome is available is diploid, and that the one would only align RNA-seq of one individual (one sample).
Or do you guys know any other pos-assembly draft error-correctors?
Thank you, guys!