I'm working on downloading the SILVA database to process my 18S data with QIIME. I understand that there are a few options here, but I'm having trouble understanding which one to choose. Is it best to download version 138 formatted with RESCRIPTr or version 132 on the SILVA website?
Thanks in advance.
It is best to use the latest version of SILVA for QIIME 2 via RESCRIPt. You can use RESCRIPt to download and curate the SILVA 138.1 database as you'd like. You can follow the general SILVA tutorial.
I forgot to mention that the choice of files depends on which tool you'd like to use to identify your sequences. The 'classifier' files are for use with
feature-classifier classify-sklearn, while the sequence and taxonomy files are provided if you'd like to use either
feature-classifier classify-consensus-vsearch or
feature-classifier classify-consensus-blast to identify your reads.