An example DADA2 workflow in R for a paired-end Illumina MiSeq 16S rRNA study across multiple runs, as well as a hand-ff to Phyloseq in R to remove contamination by negative controls.
This is by no means an official tutorial, and much of this code I got from the official tutorials. Since my dataset was rather complicated for a typical 16S run, I thought other users would benefit from this example. Feel free to reuse in good faith, and let me know if you find any typos!