text: user5190: This page is claimed to contain a gold standard benchmark for viral genome assembly.
  https://github.com/cbg-ethz/5-virus-mix
  The claim is here:
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/
  
  Baaijens et al. De novo assembly of viral quasispecies using overlap graphs
  Genome Research 2017 May; 27: 835–848.
  
  "This data set was recently presented as a gold standard benchmark (Di Giallonardo et al. 2014)"
  But at (Di Giallonardo et al. 2014) I can only find that mention:
  "We previously estimated the frequencies of the virus strains in the 5-virus-mix by amplifying the protease gene using single-genome amplification (SGA), the current gold standard for studying diversity of virus populations".
  That doesn't seem to mean precisely that the dataset is a gold standard benchmark for genome assembly but, as I understand, that SGA is a gold standard for something else.
  My question is: is it? And who decided it is? Is still valid? Is there an official list of results somewhere for this benchmark set?
  I tried to contact the owner of the page but still no answer.
  
  user77: Anyone can declare anything to be a "gold-standard", the term is meaningless. All if actually means is, "we think this is the test that everything else should be benchmarked against".
  
  user3848: Thanks for raising the issue, it is certainly topical. The question is whether the data set they unit tested is reliable.
  I think the issue they are trying get to is mosaic artefacts in the sequencing process and assembly thereon. This would be particularly true in a situation of de novo assembly which is what the authors are targeting. There are some slick methodologies for virus sequencing, which have been around for a while now, so in any case a 'gold-standard' would be outdated at present.
  I do have to agree with you that the language particularly for the journal certainly could have phrased better. The data set was 2014 and genome circularisation (its a virus small genomes) to remove the otherwise high SNP error rate would have been around in 2017 when this was published.
  I fully understand why the authors choose this language. A professional editor, not affiliated with the journal (without up to date technical insight), would likely recommend the same language.
  I guess the question would be whether verification is achieved on other virus data sets. There is no shortage of them at present and its certainly an interesting tool.
  
original_text: 5190: <p>This page is claimed to contain a gold standard benchmark for viral genome assembly.
  <a href="https://github.com/cbg-ethz/5-virus-mix" rel="nofollow noreferrer">https://github.com/cbg-ethz/5-virus-mix</a></p>
  <p>The claim is here:
  <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/</a></p>
  <blockquote>
  <p>Baaijens <em>et al</em>. De novo assembly of viral quasispecies using overlap graphs
  Genome Research 2017 May; 27: 835–848.</p>
  </blockquote>
  <p>&quot;<em>This data set was recently presented as a gold standard benchmark (Di Giallonardo et al. 2014)</em>&quot;</p>
  <p>But at (Di Giallonardo et al. 2014) I can only find that mention:</p>
  <p>&quot;We previously estimated the frequencies of the virus strains in the 5-virus-mix by amplifying the protease gene using single-genome amplification (SGA), the current gold standard for studying diversity of virus populations&quot;.</p>
  <p>That doesn't seem to mean precisely that the dataset is a gold standard benchmark for genome assembly but, as I understand, that SGA is a gold standard for something else.</p>
  <p>My question is: is it? And who decided it is? Is still valid? Is there an official list of results somewhere for this benchmark set?</p>
  <p>I tried to contact the owner of the page but still no answer.</p>
   77: <p>Anyone can declare anything to be a &quot;gold-standard&quot;, the term is meaningless. All if actually means is, &quot;we think this is the test that everything else should be benchmarked against&quot;.</p>
   3848: <p>Thanks for raising the issue, it is certainly topical. The question is whether the data set they unit tested is reliable.</p>
  <p>I think the issue they are trying get to is mosaic artefacts in the sequencing process and assembly thereon. This would be particularly true in a situation of <em>de novo</em> assembly which is what the authors are targeting. There are some slick methodologies for virus sequencing, which have been around for a while now, so in any case a 'gold-standard' would be outdated at present.</p>
  <p>I do have to agree with you that the language particularly for the journal certainly could have phrased better. The data set was 2014 and genome circularisation (its a virus small genomes) to remove the otherwise high SNP error rate would have been around in 2017 when this was published.</p>
  <p>I fully understand why the authors choose this language. A professional editor, not affiliated with the journal (without up to date technical insight), would likely recommend the same language.</p>
  <p>I guess the question would be whether verification is achieved on other virus data sets. There is no shortage of them at present and its certainly an interesting tool.</p>
  