How to do multiplex of Ion torrent sequences

Hi @khemlalnirmalkar -

If your reads are already demultiplexed, there is no need to worry about barcodes (just make sure they have been removed from your demultiplexed reads). Please see my post above about importing these demultiplexed reads.

Since these reads are already technically "joined", you won't be able to use q2-dada2 (since that plugin requires your reads be unjoined), and you are also not able to use q2-deblur, since that tool only works with Illumina products. That leaves you with OTU clustering as the only available method for generating a feature table.

I hope that helps - let us know if you have any questions. Thanks!