text: user14030: I'm trying to decide between PacBio HiFi or Illumina sequencing platforms for sequencing the genome of aChrysina scarab. We want to identify the color pattern loci and also perform a phylogenetic analysis as we'll be sequencing several species of that genus.
  When considering a hybrid approach I was told by someone at a sequencing facility that adding short reads to polish the HiFi reads assembly lowers the quality of the assembly and introduces more errors that corrections. Why is this? I haven't been able to find this statement in the literature.
  
  user37: HiFi reads can resolve most repeats in a genome. Illumina reads from these repetitive regions are likely to get mismapped and these mapping errors may become consensus errors. Most short-read polishing tools developed in the old days (e.g. pilon) will reduce the contig consensus quality. Furthermore, when you have a non-inbred diploid genome, HiFi reads can locally phase a large portion of the genome, while Illumina reads are likely to cancel/discard most HiFi phasing information, which would lead to a worse and less informative assembly.
  In theory, if you use Illumina reads the right way, you can further improve HiFi contig consensus like what the telomere-to-telomere team is doing here. However, this pipeline is for haploid/inbred genomes only. There are no tools for generic genomes. Developing your own is beyond the capability of most people in the field. To this end, the person at your sequencing facility is mostly right: don't polish HiFi assemblies with Illumina reads.
  
original_text: 14030: <p>I'm trying to decide between PacBio HiFi or Illumina sequencing platforms for sequencing the genome of aChrysina scarab. We want to identify the color pattern loci and also perform a phylogenetic analysis as we'll be sequencing several species of that genus.</p>
  <p>When considering a hybrid approach I was told by someone at a sequencing facility that adding short reads to polish the HiFi reads assembly lowers the quality of the assembly and introduces more errors that corrections. Why is this? I haven't been able to find this statement in the literature.</p>
   37: <p>HiFi reads can resolve most repeats in a genome. Illumina reads from these repetitive regions are likely to get mismapped and these mapping errors may become consensus errors. Most short-read polishing tools developed in the old days (e.g. pilon) will reduce the contig consensus quality. Furthermore, when you have a non-inbred diploid genome, HiFi reads can locally phase a large portion of the genome, while Illumina reads are likely to cancel/discard most HiFi phasing information, which would lead to a worse and less informative assembly.</p>
  <p>In theory, if you use Illumina reads the right way, you can further improve HiFi contig consensus like what the telomere-to-telomere team is <a href="https://github.com/arangrhie/T2T-Polish/blob/master/doc/T2T_polishing_case_study.md" rel="nofollow noreferrer">doing here</a>. However, this pipeline is for haploid/inbred genomes only. There are no tools for generic genomes. Developing your own is beyond the capability of most people in the field. To this end, the person at your sequencing facility is mostly right: don't polish HiFi assemblies with Illumina reads.</p>
  