GG2 with V4-V5 primers 515FB-926R vs 2021 Silva

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1

Hi everyone! Thank you so much for your amazing work.

I have a question, I bave built a library with the V4-V5 primers 515FB-926R ( --p-f-primer GTGCCAGCMGCCGCGGTAA
--p-r-primer CCGYCAATTYMTTTRAGTTT ).
I have tried several training attempt with the newest greenegen2 classifier and also tried to assign taxonomy with the full lenght classifier following the advice of a previous topic Greengenes 2 with 515F-926R primers )

However in a couple of libraries that I have been analyzing this lead to way worse taxa assignment than doing the same thing with the 2021 Silva classifier trained on the same primers. I want to use the latest GG2 classifier, but I wonder whether using those primers means that GG2 simply doesn't perform as well as Silva, or if I am misusing it.

Thank you!
Fred

3

Hi @fred-montini ,
Could you share QZVs, e.g., barplots of your results? And some description of what you expect to see/why you would say one classification is necessarily better/worse that the other?