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.