How to deal with heterozygosity during polishing of genome assembly based on long reads? All the long-read sequencing platforms are based on single-molecule sequencing which causes higher per-base error rates. For this reason a polishing step was added to genome assembly pipelines - mapping raw reads back to assembly and correcting details of the assembly.

I have decent PacBio RSII dataset of single individual genome of heavily heterozygous non-model species. Assembly went well, but when I tried to polish the assembly using quiver it could not converge over a couple of iterations and I bet it is because of too great divergence of haplotypes.

Is there any other way to polish a genome with such properties?
For instance, is there a way to separate long reads by haplotype, so I could polish using one haplotype only?
A few possibilities:

Falcon

Try falcon and falcon-unzip. These are designed exactly for your problem and your data: https://github.com/PacificBiosciences/FALCON

Not Falcon

If you think you have assembled haplotypes (which seems reasonable to expect given enough coverage), you should be able to see the two haplotypes by just doing all pairwise alignments of your contigs. Haplotypes should show up as pairs of contigs that are MUCH more similar (even with a lot of between-haplotype divergence) than other pairs. Once you have all such pairs, you can simply select one of each pair to polish.