Classifier for 16S rRNA gene(V1-V9)

[Nicholas_Bokulich]

Hi @lisadim,
For multi-primer panels see this advice (which applies to all panels, not only the brand discussed there):

How to train a classifier for paired end reads from QIAseq 16S/ITS Panel data using QIIME2 feature classifier

You could make one classifier for each primer pair. At the very least, you should make separate classifiers for ITS and 16S, but you could also use a full-length 16S classifier (e.g., one of the pre-trained classifiers on the QIIME 2 website) to classify all of the 16S domains simultaneously. Judging from the Qiagen website, it appears that they split the different primer pairs into separate datasets and classify these separately. So I recommend you do the same. If primers are present in you…