text: user10791: The vertebrate genome project (VGP)
  has a lot of interesting publications such as this one.
  The rough pipeline is outlined below:
  
  Here the pipeline in more detail:
  
  While the paper describes all the steps of the iterative assembly pipeline, I cannot find information on the runtime of their assembly-pipeline.
  I was excited to check out their github page to find out more in the documentation. Unfortunately did I not find any information on the runtime in the https://github.com/VGP/vgp-assembly repo.
  I'have written some e-mails asking collaborators of VGP but I have still not gotten any answers.
  Did any of you apply this assembly-pipeline?
  Could anyone tell me the runtime of the assembly-pipeline?
  I hope this question is in the appropriate stackexchange, if not please point me to what you think fits best. Thanks for your suggestions, please be gentle I'm new to all of this.
  For more info on the VGP check out this link
  
  user2108: Note to OP that your tag of @user172818 was not successful in your last comment. That's probably why they didn't respond.
  Because no one has gone there so far, I will simply link to HiFiAsm. See linked Nature Methods paper. This tool accepts HiFi reads, which are now standard, and gives you a GFA that you can quite easily convert to FA.
  Polishing with Illumina would actively harm the assembly, as it would remove real heterozygosity or add errors where Illumina reads map ambiguously.
  Run "out of the box"t with default options on HiFi it will probably give you much better results than VGP, haplotype-resolved.
  If you also add Hi-C PE reads with no additional options, it will give you something much much better than VGP.
  It's great. See the docs for practical info on running it.
  There is no reason to follow VGP workflows, as they are very very outdated, as pointed out in comments.
  
original_text: 10791: <h1>The vertebrate genome project (VGP)</h1>
  <p>has a lot of interesting publications such as <a href="https://www.biorxiv.org/content/10.1101/2020.05.22.110833v1.full" rel="nofollow noreferrer">this one</a>.</p>
  <p>The rough pipeline is outlined below:</p>
  <p><img src="https://www.rockefeller.edu/research/uploads/www.rockefeller.edu/sites/8/2018/01/DNAnexus.png" alt="" /></p>
  <p>Here the pipeline in more detail:</p>
  <p><img src="https://training.galaxyproject.org/training-material//topics/assembly/images/vgp_assembly/VGP_Pipeline.png" alt="" /></p>
  <p>While the paper describes all the steps of the iterative assembly pipeline, I cannot find information on the <strong>runtime</strong> of their <strong>assembly-pipeline</strong>.</p>
  <p>I was excited to check out their github page to find out more in the documentation. Unfortunately did I not find any information on the runtime in the <a href="https://github.com/VGP/vgp-assembly" rel="nofollow noreferrer">https://github.com/VGP/vgp-assembly</a> repo.</p>
  <p>I'have written some e-mails asking collaborators of VGP but I have still not gotten any answers.</p>
  <p>Did any of you apply this assembly-pipeline?
  Could anyone tell me the runtime of the assembly-pipeline?</p>
  <p>I hope this question is in the appropriate stackexchange, if not please point me to what you think fits best. Thanks for your suggestions, please be gentle I'm new to all of this.</p>
  <p>For more info on the VGP check out <a href="https://www.rockefeller.edu/research/vertebrate-genomes-project/technology-pipeline-and-policies/" rel="nofollow noreferrer">this link</a></p>
   2108: <p>Note to OP that your tag of @user172818 was not successful in your last comment. That's probably why they didn't respond.</p>
  <p>Because no one has gone there so far, I will simply link to <a href="https://github.com/chhylp123/hifiasm" rel="nofollow noreferrer">HiFiAsm</a>. See linked Nature Methods paper. This tool accepts HiFi reads, which are now standard, and gives you a GFA that you can <a href="https://www.biostars.org/p/169516/" rel="nofollow noreferrer">quite easily convert to FA</a>.</p>
  <p>Polishing with Illumina would actively harm the assembly, as it would remove real heterozygosity or add errors where Illumina reads map ambiguously.</p>
  <p>Run &quot;out of the box&quot;t with default options on HiFi it will probably give you much better results than VGP, haplotype-resolved.</p>
  <p>If you also add Hi-C PE reads with no additional options, it will give you something much much better than VGP.</p>
  <p>It's great. See the docs for practical info on running it.</p>
  <p>There is no reason to follow VGP workflows, as they are very very outdated, as pointed out in comments.</p>
  