QIIME 2 Pipeline Code Generator: A Shiny App for Automating Taxonomic Analysis Commands

High-throughput 16S rRNA gene sequencing has become a cornerstone of microbiome research, but executing complex analysis pipelines like QIIME 2 can be challenging for researchers unfamiliar with command-line interfaces. Here we present a Shiny-based web application, the QIIME 2 Pipeline Code Generator, which simplifies the construction of QIIME 2 commands for taxonomic analysis and visualization. Focusing on the initial stages of a typical QIIME 2 workflow – from post-demultiplexing sequence processing to taxa bar plot generation – our tool provides an interactive graphical interface for specifying input files and parameters. In real time, it produces a ready-to-run shell script of QIIME 2 commands that performs sequence denoising with DADA2, generates feature tables and representative sequences, assigns taxonomy with a pre-trained classifier, and creates interactive taxonomy bar plot visualizations. By eliminating manual command scripting, the application reduces syntax errors and lowers the barrier of entry for biologists, microbiologists, and other scientists who may lack advanced programming skills. The tool has been adopted by approximately 20–40 researchers at our institution, highlighting its utility in improving the accessibility and reproducibility of microbiome data analysis. We describe the motivation, design, and usage of the code generator, and discuss its role in bridging the gap between powerful bioinformatics platforms and the broader scientific community.