I want to use mothur and the SILVA_123 database to classify some full 16S PacBio data (1600 bp). Since i have long reads i thought i may be able to reach a deeper taxonomic level for several of the OTUs. Is there a curated version of the SILVA_123 I could download that goes to the species level?
No there isn’t - you’d have to do this. Also, greengenes, which is held up as a model for including species-level data only has that information for ~11% of sequences. Considering so many of the reads in databases are from culture-independent approaches where we rarely know the true species name, I think this might be a fool’s errand.