Vsearch Taxonomy Assignment After DADA2

Hi,

I’m curious that if I want to do denoise with DADA2 and get ASV from DADA2, so further if I do 97% OTU picking with Vsearch Cluster,

qiime vsearch cluster-features-closed-reference

According to this, I can just use

biom add-metadata

to add the taxonomy annotation to the 97% OTU instead of using

qiime feature-classifier classify-consensus-vsearch

What I understood is if I want to do taxonomy assignment with 97% OTU table, “biom add-metadata” would work the same as “qiime feature-classifier classify-consensus-vsearch”.

What if I want to use “qiime feature-classifier classify-consensus-vsearch” to do taxonomy assignment on ASV with 97% reference taxonomy file and 97% OTU file, would it work the same as using “biom add-metadata” to add taxonomy annotations to 97% OTU table?

Many Thanks

That is incorrect. Using biom add-metadata as described in that forum post adds the taxonomy labels of the reference OTU to which your OTUs clustered… but that does not necessarily mean it is a perfect match and that taxonomy label is correct. See here and here for details.

classify-consensus-vsearch performs the same global sequence alignment (using vsearch), but grabs the top N hits and then assigns the LCA consensus taxonomy among those (using separate code not associated with vsearch, and hence distinct from cluster-features-closed-reference). See here for a description of this process.

That post you linked to is specific for sending QIIME2-processed data off to picrust, where reference-based OTU clustering is essential for clustering sequences against ref seqs from fully sequenced genomes. It is not a recommendation for general practice.

No. It would assign the most likely taxonomy to each sequence, taking into account consensus among top hits (the idea being that you could have multiple close matches that have different taxonomy assignments! So a close match to the top hit does not make that the “correct” taxonomy).

I hope that helps!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.