Naive Bayes classifier for the 515F/806R region

Hi,

I used the Naive Bayes classifier trained on primers 515F/806R available on Data resources — QIIME 2 2022.2.0 documentation. I recently notice that in the earth microbiome protocol their are two versions of primer for the 515F/806R regions.

Updated sequences: 515F (Parada)–806R (Apprill), forward-barcoded:
FWD:GTGYCAGCMGCCGCGGTAA; REV:GGACTACNVGGGTWTCTAAT
Original sequences: 515F (Caporaso)–806R (Caporaso), reverse-barcoded:
FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT

After a thorough search on qiime forum and internet I did not find information regarding which primer set was used to train the classifier. Had you inform if the this classifier used the updated or original sequences?\

Best regards,
Antonio

Hi @Antonio_Louvado, welcome to :qiime2:!

You can determine this by looking through the provenance information of the silva-138-99-515-806-nb-classifier.qza file. That is, simply drag-drop this file into QIIME 2 View, then click on the provenance tab. From here you can click on each item in the provenance graph to see what parameters were used for each command. Like this:

Here you can see, the primer sequence that where used. It looks like the original primer sequences where used.

Personal note: The only difference between these two primer sets is the additional IUPAC ambiguity bases in the "updated" primer sequences. When I make the classifier I use the "updated" primer set, as they are more "universal" than the original sequences. Which means better success in finding and searching for your amplicons.

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Thanks very much for the information.

Antonio

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