Good morning! We have been training our feature classifier on our own data as recommended in the qiime2 docs (“taxonomic classification accuracy of 16S rRNA gene sequences improves when a Naive Bayes classifier is trained on only the region of the target sequences that was sequenced (Werner et al., 2012)”). However, for the sake of comparison we also performed taxonomic analysis on pre-trained classifiers as shown below. You can see the classification resolution varied dramatically, and we are unsure of whether using a self-trained classifier is actually the most appropriate method.
We appreciate any guidance the qiime2 community can give us! Thanks.