Phyloseq workflow for microbial community analysis

Complete, fully reproducible phyloseq workflow for 16S rRNA microbiome
analysis of the Bocas del Toro hypoxic event. Included are the HTML and
Rmarkdown (.Rmd) files plus the output of the DADA2 pipeline in Rdata format
which is the main input file for the phyloseq workflow.

Sequences were filtered and dereplicated. Sequence variants were called and
putative chimeras identified. Sequence variants were classified using SILVA
and GreenGenes databases. File contains a sequence table and taxonomy table.
We imported this file directly into phyloseq for community analysis.

The MANUAL_INPUT.zip directory contains all of the additional input files
(mainly tables) necessary to run this workflow. Please note script will create
a directory called **R_OUTPUT** wherever the .Rmd file was called from. This
is where the script will store output files.