AMPBA-workflow

Amplicon metabarcoding, the high-throughput sequencing of taxonomically informative marker gene sequences, is now standard for biodiversity assessment and environmental monitoring. These markers differ in target taxa, evolutionary rate, and resolution, so no single fixed strategy fits all of them. A typical workflow chains many steps, from read preprocessing through denoising or clustering, taxonomic assignment, and statistical filtering, each requiring its own methodological decisions. Combining these into one coherent, reproducible pipeline is a persistent challenge: solutions tend toward either flexible but poorly documented single-use scripts, or standardized but rigid, often infrastructure-heavy platforms. AMPBA occupies the middle ground: a locally installable, easy-to-use, workflow-managed pipeline that treats each stage of feature creation and manipulation as an optional module. This modularity supports a wide range of markers, analysis strategies, and study designs, while keeping results reproducible across computing environments and repeated runs.