How to demux dual-indexed reads

User Support
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Hi @thermokarst,

I’m a newbie to QIIME2 and just installed QIIME2 2018.8.
Been jumping from post to post looking for solutions but I haven’t got any yet :frowning:

I have 16S data with adapters in both forward and reverse reads. I can’t find any other post about dual-indexing these reads with cutadapt.
Any updates on this functionality in QIIME2 2018.8 and “how” to go about this…In case this isn’t implemented?? Because I need to remove adapters for both reads.

I’m hopeful for a solution. Thanks for your help.

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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.

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