Do you need to BLAST sequences classified with a SILVA classifier?

I have paired-end 16S sequences that I have taxonomically classified with a SILVA database classifier.
Is there any benefit to using NCBI to blast the sequences as well? I guess it could potentially provide more phylogenetic information but couldn’t it also provide hits for anything that matches?

Hi @Ellenphant,

A naive Bayes classifier trained on the SILVA database using q2-feature-classifier? Great! As long as the results look good, that should be all you need.

Only if you need a second opinion or want to figure out what some unclassified reads are. NCBI BLAST can be quite misleading for taxonomic classification as I’ve described here:

Exactly! So you need to look carefully to see how similar those hits are, and whether you have multiple ties for top hit. It gets messy, which is why we have methods in q2-feature-classifier to do the job for you. :man_factory_worker:

I hope that helps!

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