I am currently planning on running some new 16S samples with SILVA138 trimmed to the primer region and I downloaded the qza files from this previous thread (which was very helpful!).
However, I am a bit confused whether I should use the consensus classifier or just the regular one? Can someone explain the difference?
As you can see from the note at the top of that thread, those instructions have been replaced by a more recently released plugin. I recommend you follow the link to that tutorial to use the most up-to-date methods.
But if you just want pre-trimmed sequences and/or pre-trained classifiers, the latest versions (with SILVA 138) are available from the QIIME 2 data resources.
These are two entirely different methods for taxonomy classification. I recommend reading (1) the documentation (help docs, Q2 website) or (2) the primary literature on the topic to better understand the inner workings of q2-feature-classifier:
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