training classifier SILVA: what is the best way?

[SoilRotifer (Mike Robeson)]

Hi @Silke_Lambert,

@Silke_Lambert

And is it okay to not use any curation steps? will the classification be accurate?

The SILVA tutorial is only meant to show what is possible with RESCRIPt, it's not necessarily an SOP. Curate as you think is appropriate.

That being said, at the very least, qiime rescript cull-seqs ... and qiime rescript dereplicate ... should be run prior to constructing the classifier. There are some poor quality sequences (some contain many ambiguous or missing bases) within the database, which should probably be removed, as they may interfere with classification.

-Cheers!