microbiota analysis of insect species

Hi @Linda_Abenaim
I would recommend this tutorial: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt

It should walk you though all the steps.

My preferences for databases is GTDB, but that's a preference thing. Silva is not exclusively 16S, so its pretty big and takes a while to run. If you want to use Greengenes2 (which uses GTDB and some), this post explain using Greengenes2 Classifier: Introducing Greengenes2 2022.10

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