Hi, I’m looking for some guidance on how to interpret the ‘Confidence’ column for taxonomic assignments obtained using
classify-sklearn (if it matters, I have been using the classifier pre-trained on trimmed 99% OTUs from Greengenes).
I see that there was another post on this topic in 2017, but since the answer then indicated that the notion of confidence was under devlopment, and I also noticed the default value for
--p-confidence parameter in the current version of the
classify-sklearn plugin differs from what is described in the answer to that question, I was hoping to get an updated response.
Can we interpret the Confidence value as % sequence identity to the reference sequence for the taxon an ASV is assigned to (i.e. 1 is 100% sequence identity to the reference sequence, 0.95 is 95% sequence identity), or is there something else going on?