I used the genebank for taxonomic classification and some samples came out with a confidence level of 70%. Wouuld this be acceptable? Would you recommend trying Silva?
Hi @Rsimmonds,
Is this the confidence level of the classify-sklearn method in q2-feature-classifier?
If so, then yes that is acceptable. This confidence threshold is what the classifier uses to decide if classification at a specific rank is accurate enough to apply a label. So you can interpret that as "this sequence almost certainly belongs to genus X, and we are 70% confident it is this species". This 70% threshold was optimized through a series of tests, you can read more about this method here:
And by the way you can always modify the confidence threshold with the --p-confidence parameter in classify-sklearn... but read the paper first to understand what that will do to your results!
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