I am analyzing my samples with Ion Torrent sequencer and have the following question. The thing is that the kit sequences 7 hypervariable regions and I want to compare the results I get in Qiime2 (about those 7 regions) with the ones obtained using the Ion Reporter software.
This Ion Reporter software gives the taxonomic results by regions or using a consensus of all the regions, where the results of each regions are added up. My questions is if the command classify-consensus-vsearch does a similar consensus or not, as I am analyzing 7 regions instead of one.
The “consensus” in this method stands for something else: it means that the taxonomic ID (of each individual read) is assigned based on the consensus taxonomy of the top hits, not a consensus of the separate regions (which sounds more like a sum of the results from each read, rather than a consensus per se based on your description).
But the equivalent could be accomplished, by using the full-length 16S rRNA gene sequences as a reference and analyzing all the data together.
This and other related topics are discussed in this long but informative topic: