Hello!
I want to change the phyla names, for example Actinobacteriota on Actinomycetota, etc, accordingly to new classification on
how can i do that?
I used silva-138-99-515-806-nb-classifier.qza to get the taxonomy with qiime2 pipeline, but I got old names.
I do some visualization creating phyloseq object in Rstudio, but still havent found anything to fill this issue.
I think classifieres are not updated. Is is possible to get a total new version of silva-138-99-515-806-nb-classifier.qza?
Thank you
You can use RESCRIPt to curate your SILVA database, and use its edit-taxonomy action to edit the SILVA taxonomy file prior to training the classifier.
Otherwise, you can also use RESCRIPt's get-gtdb action to make your own GTDB database. Which uses many of these new naming conventions, though is not quite as expansive as SILVA.