I could not found any tutorial that shows how to join paired ends of demultiplexed data. I tried to join each sample individually using “Atacama soil microbiome” tutorial, but it did not worked, cause it needs a barcode file. How can I do it?
Hi @Flavio! If you are planning to use q2-dada2 for quality control, you don’t need to worry about joining your paired-end data - DADA2 does that for you as part of its process! You will need to import your unjoined paired-end data first: you can follow the Import Tutorial for more help. There are a few relevant sections, you will need to pick the choice that is most appropriate for your data: Casava 1.8 formatted data, or the more general-purpose “Fastq Manifest Format.” Good luck and keep us posted! 
As a follow up.
After the qiime dada2 denoise-paired command the output files correspond to sequences that have been joined. Is that correct?
Kind regards
George
Hi @George_Tsiamis! Yes, you’re correct that the sequences output by qiime dada2 denoise-paired have been joined. Those sequences are Amplicon Sequence Variants (ASVs) and are intended to represent the actual biological sequences in your data. Those sequences will be stored in a QIIME 2 Artifact (.qza file) with the FeatureData[Sequence] semantic type.
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The QIIME 2 2017.11 release has expanded support for analyzing paired end reads! See the paired end reads community tutorial for more details. 
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