decontam: what DNA concentrations should I used?

Library Plugin Support
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Dear colleagues,

I have a couple of questions regarding the application of Decontam that remain unclear after reading the paper and the plugin tutorial:

  1. In the case of using the prevalence method, what is the minimum number of controls ("blanks" of DNA extraction) recommended? If I’m not mistaken, the paper mentions a minimum of 5-6 controls and advises using more to increase sensitivity. However, in my experience, I unfortunately don’t usually have access to that many extraction controls (typically 1-3 controls per run).

  2. When opting for the frequency method, which DNA concentration should be used? Should it be the concentration from the extract or the concentration of the libraries (sometimes provided by the sequencing service)?

Thank you very much and best regards,
Jose

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Hey @jordenrabasco, any suggestions for @ja.morillo?

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Hi @ja.morillo!

  1. When using the prevalence method, 5-6 controls would be preferable however if this is not possible, we recommend using at least 3 controls per 96 samples or more if you have low concentration samples.
  2. When using the frequency method the concentration from the libraries or the DNA extraction concentration can be used. You just need to supply enough samples to produce a gradient of concentrations to fulfill the assumptions of the method.

Thanks for your interest in Decontam and let me know if you have any more questions!

best,

Jorden Rabasco

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Hello,
Thanks a lot for your help and for developing decontam and the plugin. Then, I will try a combination of both methods, using 3 controls and DNA extracts concentrations.
Best regards,
jose

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