text: user57: 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?
  
  user73: You could also have a go at Canu. It's designed for long-read assembly (both PacBio and Nanopore), although not specifically for complex population sequencing. It tries to strip a genome down into its unique components, and generates paths from those components that are well-supported from the reads.
  With regards to polishing, it seems to be the case that polishing doesn't converge, and there will be a lot of variants that just oscillate between two possibilities. For me and at least one other person at London Calling this year, there was basically no gain in accuracy for polishing past the third iteration. I used my own error correction algorithm, but they used the more "standard" polishing with Pilon. For what it's worth, the nanopore WGS consortium used Racon for polishing their Canu assemblies.
  
  user156: 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.
  
original_text: 57: <p>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.</p>
  
  <p>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 <a href="https://github.com/PacificBiosciences/GenomicConsensus" rel="noreferrer">quiver</a> it could not converge over a couple of iterations and I bet it is because of too great divergence of haplotypes.</p>
  
  <p>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?</p>
   73: <p>You could also have a go at <a href="https://github.com/marbl/canu/releases" rel="nofollow noreferrer">Canu</a>. It's designed for long-read assembly (both PacBio and Nanopore), although not specifically for complex population sequencing. It tries to strip a genome down into its unique components, and generates paths from those components that are well-supported from the reads.</p>
  
  <p>With regards to polishing, it seems to be the case that polishing doesn't converge, and there will be a lot of variants that just oscillate between two possibilities. For me and at least one other person at London Calling this year, there was basically no gain in accuracy for polishing past the third iteration. I used my own error correction algorithm, but they used the more "standard" polishing with Pilon. For what it's worth, the nanopore WGS consortium used Racon for polishing their Canu assemblies.</p>
   156: <p>A few possibilities:</p>
  
  <p><strong>Falcon</strong></p>
  
  <p>Try falcon and falcon-unzip. These are designed exactly for your problem and your data: <a href="https://github.com/PacificBiosciences/FALCON" rel="nofollow noreferrer">https://github.com/PacificBiosciences/FALCON</a></p>
  
  <p><strong>Not Falcon</strong></p>
  
  <p>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.</p>
  