Hi all, just an FYI:
Here are new locations for the updated SILVA taxonomy (i.e. Greengenes-like) reference files for both the SSU and LSU data. To save space and bandwidth, these are the raw FASTA and TSV files. So, you’ll have to import and train them yourself. Be sure to read the SILVA License.
Be wary of the species labels. For example, there are a few taxa annotated with a species label that corresponds not to the organism to which the sequence belongs, but from the source material from which the sequence was obtained. Here is an example:
d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Serratia; s__Oryza_sativa_Indica_Group_(long-grained_rice)
d__Eukaryota; p__Arthropoda; c__Insecta; o__Hemiptera; f__Hemiptera; g__Hemiptera; s__Oryza_sativa_Indica_Group_(long-grained_rice)
As you can see, we have an insect and a bacterial sequence both annotated with the species label Oryza sativa (rice). In most cases the species rank information seems okay, but there are enough issues like the one above, that convinced me to generally be cautious of the species label.
Anyway, I hope these are useful.
-Best wishes!
-Mike