Hi there @tunski!
Are your barcodes still in the reads? If so, check out the q2-cutadapt tutorial for guidance on importing and demultiplexing these reads. Once demultiplexed, you can choose whatever pipeline makes sense to you (e.g. Moving Pictures tutorial).
If your barcodes are somewhere else (as in, not in the reads), give us some more details (maybe a few lines from one or both files), that way we can provide some more targeted guidance.
Thanks! 
