feature classifier full length sequences

Good day,
I would like to ask if a full length greengenes trained classifier is better than a V3-V4 trained classifier, for the taxonomy of 16S rRNA sequences generated with V3-V4 primers?
Thank you in advance

Hi,

As mentioned in the QIIME2 tutorial, Training feature classifiers with q2-feature-classifier, “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).” Thus, a feature classifier trained on the V3-4 regions should give you better results.

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