Introduction Set Up Your Environment The Microbiome Data Download and Install necessary R packages Set up Working Environment Reads The Analysis Check Read Quality Read Filtering Learn the Error Rates and Infer Sequences Merge Forward and Reverse Reads Construct Sequence Table Remove chimeras Tracking Reads throughout Pipeline Assign Taxonomy Information Phyloseq Object Taxonomic Filtering Prevalence Filtering Visualization / Diversity Phylum Relative Abundance Genus Relative Abundance Introduction The purpose of this post will be to guide researchers through a basic analysis of microbiome data using R packages DADA2 and Phyloseq.