text: user180: I would like to know what do people verify when designing/using spike-in controls, to be used in sequencing experiments (mainly Illumina). So far I came up with this list:
  
  Does it align only to a given genome synthetic reference?
  Does it contain G-quadruplexes? E.g. QGRS Mapper
  Does it contain known Illumina error motifs? (Do this matter anymore for recent platforms/chemistries?) See this article
  Does it contain other motifs known to be polymerase inhibitors? Ref
  
  Anything else?
  
  user174: Disclaimer: I'm a developer for http://www.sequin.xyz.
  Sequin is a new set of spiked-in controls for next-generation sequencing, and that includes Illumina. We design controls for RNA-Seq, genome sequencing, metagenomics etc.
  Please study our papers if you want more details.
  
  Reference Standards For Next-Generation Sequencing by Hardwick should be a good start. 
  
  Here's my list:
  
  Measured counts against input concentration. Pearson's correlation, spearman correlation and regression slope.
  PCA analysis
  Whether the synthetic aligned to the synthetic reference
  Spiked-in amount (e.g. dilution)
  Diagnostic statistics
  ROC Curve
  Detection limit
  
  (1) is important because the controls should give you correlation = 1, and slope = 1 in a perfect flawless experiment. This is a sample output (you can read more about it in our papers):
  
  (2) This is our sample PCA (our paper has the details)
  
  (3) is also important but you can only do that in simulations.
  (5)
   
  (6)
  
  (7)
  
  
original_text: 180: <p>I would like to know what do people verify when designing/using spike-in controls, to be used in sequencing experiments (mainly Illumina). So far I came up with this list:</p>
  
  <ul>
  <li>Does it align only to a given genome synthetic reference?</li>
  <li>Does it contain G-quadruplexes? E.g. <a href="http://bioinformatics.ramapo.edu/QGRS/index.php" rel="nofollow noreferrer">QGRS Mapper</a></li>
  <li>Does it contain known Illumina error motifs? (Do this matter anymore for recent platforms/chemistries?) See <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0976-y" rel="nofollow noreferrer">this article</a></li>
  <li>Does it contain other motifs known to be polymerase inhibitors? <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4923904/" rel="nofollow noreferrer">Ref</a></li>
  </ul>
  
  <p>Anything else?</p>
   174: <p><strong>Disclaimer</strong>: I'm a developer for <a href="http://www.sequin.xyz" rel="nofollow noreferrer">http://www.sequin.xyz</a>.</p>
  
  <p>Sequin is a new set of spiked-in controls for next-generation sequencing, and that includes Illumina. We design controls for RNA-Seq, genome sequencing, metagenomics etc.</p>
  
  <p>Please study our <a href="http://www.sequin.xyz/about/papers/" rel="nofollow noreferrer">papers</a> if you want more details.</p>
  
  <ul>
  <li><strong>Reference Standards For Next-Generation Sequencing</strong> by Hardwick should be a good start. </li>
  </ul>
  
  <p>Here's my list:</p>
  
  <ol>
  <li>Measured counts against input concentration. Pearson's correlation, spearman correlation and regression slope.</li>
  <li>PCA analysis</li>
  <li>Whether the synthetic aligned to the synthetic reference</li>
  <li>Spiked-in amount (e.g. dilution)</li>
  <li>Diagnostic statistics</li>
  <li>ROC Curve</li>
  <li>Detection limit</li>
  </ol>
  
  <p>(1) is important because the controls should give you correlation = 1, and slope = 1 in a perfect flawless experiment. This is a sample output (you can read more about it in our papers):</p>
  
  <p><a href="https://i.stack.imgur.com/DjqEV.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/DjqEV.png" alt="enter image description here"></a></p>
  
  <p>(2) This is our sample PCA (our paper has the details)</p>
  
  <p><a href="https://i.stack.imgur.com/vGTh0.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/vGTh0.png" alt="enter image description here"></a></p>
  
  <p>(3) is also important but you can only do that in simulations.</p>
  
  <p>(5)</p>
  
  <p><a href="https://i.stack.imgur.com/zaEfm.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/zaEfm.png" alt="enter image description here"></a> </p>
  
  <p>(6)</p>
  
  <p><a href="https://i.stack.imgur.com/cg6ss.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/cg6ss.png" alt="enter image description here"></a></p>
  
  <p>(7)</p>
  
  <p><a href="https://i.stack.imgur.com/NRF6p.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/NRF6p.png" alt="enter image description here"></a></p>
  