This repository serves as an example analysis for SWS6323 Advanced Microbial Ecology. We will use this relatively small dataset to practice running common microbial ecology analysis tasks in R. The sequencing reads used here have been trimmed of adapter and primer content on hipergator before use in R. Additional information can be found in this repository's wiki.

Sequence data can be downloaded to your local computer in two ways. If you are experienced with Github Desktop, you can clone the repository locally to your own computer. Most of you will not be familiar with Github Desktop and can therefore most easily downloaded the sequence data from this one drive directory. Download the "cutadapt" directory to your local computer. Uncompress the "cutadapt" directory locally after downloading, but do not uncompress the fastq.gz files.