Microbial Ecology Group manuscript code

This repository contains all of the code required to replicate the analysis in the manuscript "METAGENOMIC INVESTIGATION OF THE EFFECTS OF ANTIMICROBIAL DRUG USE PRACTICES ON THE MICROBIOME AND RESISTOME OF BEEF FEEDLOT CATTLE"

Table of contents

• Accessing sample reads
• Bioinformatic analysis
  • Microbiome analysis with Qiime2
  • Resistome analysis with AMR++
• Statistical analysis