text: user10791: I am reading the Whole Genome Sequencing for de novo Assembly Best Practices
  
  
  Use the Sequel II or IIe System and SMRT® Cell 8M to sequence to desired coverage depth for complexity
  of genome
  10- to 15-fold coverage per haplotype recommended
  
  
  First of all Wikipedia shows different definitions for the term haplotype. Which one applies here?
  Second while the recommendations state to use 10- to 15-fold coverage per haplotype I find myself confused about how I would know the haplotype beforehand.
  From what I understand of haplotype-estimation I would need the sequenced data first.
  How would I go about this when wanting to do a de novo assembly of a species that has no published assembly of any close relatives? That means the only information I would have at that point is the C-value of the species to be sequenced.
  Or better, how does the Sequel II figure out the number of haplotypes for achieving the desired fold-coverage?
  I hope I'm in the right SE.
  
  user37: Unless you want to reconstruct all haplotypes, you can sequence to ~30X regardless of ploidy.
  
  user2108: They just want to know the ploidy of the sample. In a diploid sample, e.g. humans, there are two haplotypes. This is mostly important for haplotype resolution (i.e. get the two full genomes in a diploid).
  Note that elsewhere in the brochure that you link it writes:
  
  Fast and efficient assembly of even
  the largest genomes with haplotype
  resolution of complex polyploids
  
  If you are working with a diploid species, that translates to 20-30X coverage. That seems low to me for the older tech of CLR/Sequel sequencing, but they are the experts.
  Different recommendations posted here by a service provider suggest 40-50X for structural variant analysis, which seems more reasonable.
  
original_text: 10791: <p>I am reading the <a href="https://www.pacb.com/wp-content/uploads/Application-Brief-Whole-genome-sequencing-for-de-novo-assembly-Best-Practices.pdf" rel="nofollow noreferrer">Whole Genome Sequencing for <em>de novo</em> Assembly Best Practices</a></p>
  <blockquote>
  <ul>
  <li>Use the Sequel II or IIe System and SMRT® Cell 8M to sequence to desired coverage depth for complexity
  of genome</li>
  <li>10- to 15-fold coverage per haplotype recommended</li>
  </ul>
  </blockquote>
  <p>First of all Wikipedia shows different definitions for the term <a href="https://en.wikipedia.org/wiki/Haplotype" rel="nofollow noreferrer">haplotype</a>. Which one applies here?</p>
  <p>Second while the recommendations state to use <code>10- to 15-fold</code> coverage per haplotype I find myself confused about how I would know the <a href="https://en.wikipedia.org/wiki/Haplotype" rel="nofollow noreferrer">haplotype</a> beforehand.</p>
  <p>From what I understand of <a href="https://en.wikipedia.org/wiki/Haplotype_estimation" rel="nofollow noreferrer">haplotype-estimation</a> I would need the sequenced data first.</p>
  <p>How would I go about this when wanting to do a <em>de novo</em> assembly of a species that has no published assembly of any close relatives? That means the only information I would have at that point is the C-value of the species to be sequenced.</p>
  <p>Or better, how does the Sequel II figure out the number of haplotypes for achieving the desired fold-coverage?</p>
  <p>I hope I'm in the right SE.</p>
   37: <p>Unless you want to reconstruct all haplotypes, you can sequence to ~30X regardless of ploidy.</p>
   2108: <p>They just want to know the ploidy of the sample. In a diploid sample, e.g. humans, there are two haplotypes. This is mostly important for haplotype resolution (i.e. get the two full genomes in a diploid).</p>
  <p>Note that elsewhere in the brochure that you link it writes:</p>
  <blockquote>
  <p>Fast and efficient assembly of even
  the largest genomes with haplotype
  resolution of complex polyploids</p>
  </blockquote>
  <p>If you are working with a diploid species, that translates to 20-30X coverage. That seems low to me for the older tech of CLR/Sequel sequencing, but they are the experts.</p>
  <p>Different recommendations posted <a href="https://pacbio.gs.washington.edu/" rel="nofollow noreferrer">here</a> by a service provider suggest 40-50X for structural variant analysis, which seems more reasonable.</p>
  