Thread: Ion Proton Q20
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Old 11-04-2013, 02:48 AM   #6
David Eccles (gringer)
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838

Originally Posted by Buzz0r View Post
Could you elaborate on how the Q30 (Ion) is != Q30 (Illumina)? I thought it is a set value showing an accuracy for base calling of 99.9% being correct (hence one error in 1000 bases).
The cause of errors is unpredictable, so it is essentially impossible to work out the precise accuracy of a given sequenced base. There are a number of things that can contribute to error; some can be measured, some can not:
  • polymerase read errors
  • wobble base pairing
  • incorrect primer binding
  • image focus
  • ion calibration
  • fluorophore overlap / bleed through
  • phasing (stochastic chemistry for base addition)
  • inadequate flow
  • irregular flow
  • electrical noise
  • optical noise
  • bubbles
  • sample contamination
  • sample degredation

[please don't consider that an exhaustive list... that's just what came to my mind in a couple of minutes]

Different systems will have different biases due to the different technology used in the system, as well as different assumptions made by the people writing the code to calculate error probability. All that can really be done is to make some guesses about what parameters are the most important, test a few models based on those parameters in real-world scenarios, choose the best model(s), and hope that your models fit the most common use cases for analysis.

In short, it would be silly for Illumina and Life Technologies to use the same method for calculating sequencing error, because of the substantially different technology behind the machines.

Last edited by gringer; 11-04-2013 at 02:51 AM.
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