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PEMA is a HPC-centered, containerized assembly of key metabarcoding analysis tools. It supports the downstream analysis of four marker genes (16S/18S rRNA, ITS and COI) but also, by allowing the user to train the classifiers with custom reference databases, it can be used for further marker genes. By combining state-of-the art technologies and algorithms with an easy to get-set-use framework, PEMA allows researchers to tune thoroughly each study thanks to roll-back checkpoints and on-demand partial pipeline execution features.