By Kelly Shannon

###This pipeline is adapted from the benjjneb dada2 pipeline found on GitHub: https://benjjneb.github.io/dada2/tutorial.html and based on Callahan et al., 2016. DADA2: High Resolution Sample Inference from Illumina Amplicon Data. Nature Methods. As well as from one created by MK English in Dr. Ryan Mueller’s lab at OSU. ##The pipeline will be performed with 14 total paired-end sequence fastq files (7 individual samples) as an example flowthrough. These are V4 hypervariable region amplicon sequences performed by the Oregon State University CGRB on an Illumina MiSeq NGS sequencer.

This tutorial aims to guide the user through a NMDS analysis of 16S abundance data using R, starting with a ‘sample x taxa’ distance matrix and corresponding metadata.

My final code here represents a wide conglomeration of script from previous Colwell Lab graduate students and my own invention.