I want to import multiplexed paired end reads but I have no barcodes.fastq.gz

[thermokarst]

Please see this community tutorial:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin,…

You will need to make a few adjustments to the commands listed there to make it work with paired-end reads. If you get stuck please check in with us here - thanks!