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?
Hi @Ellenphant,
As you can see from the note at the top of that thread, those instructions have been replaced by a more recently released plugin.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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