For taxonomic classification, we are utilizing a Naive Bayes classifier that has been pre-trained on the Greengenes and the RDP database. My ASVs are generated using the function qiime dada2 denoise-paired.
I'm curious to know if Qiime2 also supports the SILVA database.
If it does, could you kindly provide a link to a tutorial?
If you look through the documentation pages you'll find the Data resources page. Which has a collection of premade classifiers (and the files used to make them) readily available, e.g. SILVA and Greengenes2.
However, if you'd like to construct and curate your own reference database, you can check out our RESCRIPt plugin. We have tutorials for SILVA, GTDB, and RDP, and other approaches. Also, feel free to check out the new Greengenes2.
@SoilRotifer Thank you very much !!
sorry for the delay. I had trouble logging in (I lost my email password).
Does the latest version of SILVA is Silva-v13.8 ?
Yep, SILVA is at version
138. You should be able to confirm this by looking through the provenance. However, I think the premade files are not the latest version,
138.1. If you'd like to use
138.1 then you can run through the RESCRIPt tutorial and construct the reference classifier yourself... though it'll take a while. If you are running
qiime2-amplicon-2023.9, I'd suggest installing via this set of commands.