zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.

Summary: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling. Availability and implementation: Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.