Has anyone looked into how the new quality binning strategy Illumina is using on NovaSeq sequencers impacts denoising of 16S data? What are the best practices?

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Hello!
Did you already find this issue on the Dada2 github? Consequences of using dada2 on NovaSeq data · Issue #791 · benjjneb/dada2 · GitHub

So, options are:

  1. Use Dada2 R package with modifications as described by the link.
  2. Use Dada2 R or q2-Dada2 as it is, since there are several reports with not significant variations between using Dada2 as it is (R or Qiime2) and modified version
  3. Use Deblur which is not affected by changes in quality scores bining.
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