What is QIIME?

QIIME (Quantitative Insights Into Microbial Ecology) is a powerful, extensible, and open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. It's commonly used to analyze amplicon sequencing data (e.g., 16S rRNA gene) to characterize microbial communities, compare microbial diversity across different samples or experimental conditions, and identify microbial taxa associated with specific phenotypes or environments. QIIME 2 is the latest version and emphasizes reproducibility, data provenance, and plugin-based extensibility.