SILVA V4 classifier

[Nicholas_Bokulich]

Hi @valseitz ,
We decided last year to stop hosting the V4 classifiers and focus on the full-length classifiers to reduce the maintenance burden, because (a) the performance benefit is not so significant vs. full-length (other than lower RAM requirements); (b) this is only one of many primer sets used for 16S analysis; and (c) users who need classifiers trained on a specific subregion can extract that region and train their own. So I don't think the V4 classifiers will be added back.

The higher RAM required for using the full-length SILVA classifier is indeed a concern in workshops. What I have personally started using in workshops/teaching is to train NCBI RefSeqs 16S classifiers using RESCRIPt, because this is a much smaller classifier, requiring lower RAM so most students can also train it on their own laptop. But of course RefSeqs and SILVA have some design differences and will have different strengths in practice, so that's one caveat. Here's a tutorial about this if you are interested:

Using RESCRIPt to compile sequence databases and taxonomy classifiers from NCBI Genbank

This tutorial will describe how to create custom reference databases from NCBI Genbank using RESCRIPt. Read more about RESCRIPt here: Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt - #7 If using NCBI Genbank data, please be aware of the NCBI disclaimer and copyright notice. Citation: If you use RESCRIPt or any RESCRIPt-processed data in your research, please cite the following pre-print: Michael S Robeson II, Devon R O'Rourke, Benj…

Very cool to hear that you will be running a QIIME 2 workshop! When/where? You would be very welcome to announce this in the Misc category if it is an open enrollment workshop.