using classify.seqs with Silva, would that be a good
idea also to classify rRNA gene sequences from a
shotgun library?


Have you already pulled out the 16S? I guess you could align all your seqs, discard the ones that don’t align, and classify the ones that do. I haven’t tried it but would be interested to hear how long it takes

I just classified using classifiy.seqs directly against the raw shotgun reads.
Assume the ones I got classified are ok. Wondered only if something might
go wrong because of all the non ribosomal sequences present.

I’m not sure if classify seqs has a length cutoff? you may need to check into that since it’s typically used after qc.

My only comment would be to remember that everything will classify as something - regardless of whether it’s a 16S rRNA sequence or not. Might want to double check that your classify.seqs database has some type of outgroup. Also, a shotgun read may also have part of a 16S rRNA gene and another gene.