DEPRECIATED, PLEASE SEE https://github.com/jbisanz/AmpliconSeq/blob/master/analysis_scripts/QIIME2_pipeline.Rmd
The QIIME2_pipeline.Rmd is setup to run on the QB3 cluster; however, could be modified to be run on any system as it is not taking full advantage of the cluster environment. The top section of the markdown documents contains the users preferences to be pasted into your chef.compbio.ucsf.edu session.
Older versions of pipelines are available in the directory archived.