QIIME is a widely used, open-source microbiome analysis software package that converts raw sequence data into interpretable visualizations and statistical results. QIIME2 has recently succeeded QIIME1, becoming the most updated platform. The protocols in this article describe our effort in automating core functions of QIIME2, using datasets available at docs.qiime2.org. While these specific examples are microbial 16S rRNA gene sequences, our automation can be easily applied to other types of QIIME2 analysis.
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