How to demux dual-indexed reads

Hi @halt_BB,
Sorry! We do not yet have a method for demultiplexing dual-indexed reads with q2-cutadapt or q2-demux.

For now, you will need to demultiplex with another program (e.g., I believe qiime1 had a method for this), and then you can import the demultiplexed data to QIIME 2.

We hope to add a method for demultiplexing dual-indexed reads in the future, so please stay tuned as releases come out, or track this open issue. Unfortunately, there is no ETA at this time.