Hi @Martin,
thanks for your message and the scripts! I will definitely try them as they seem exactly what I need.
Thank you also for bringing to my attention the qiime1 forum discussion, I also find it very useful.
I also happen to have the reverse primers in the sequence, so I will follow the steps that you and @thermokarst described in your thread. Thank you again! They are very informative.
So, would the pipeline look like this? Extract barcodes, join reads, import your sequences to Qiime2 with the multiplexed single-end protocol, demultiplex, then trim fwd and reverse primers, deblur?
And one last question (sorry, I am not very familiar with Ilumina data yet): why wouldn't it make sense for my reads to be joined? (As a bit of background information, just in case it helps, my amplicon is 291bp long and I have used 2*251bp sequencing).
Thanks a lot again!