LEMMI (A Live Evaluation of Computational Methods for Metagenome Investigation) is an online catalogue of tools and a pipeline dedicated to the continuous benchmarking of newly published methods for shotgun metagenomic profiling. LEMMI16s is the equivalent platform for 16S rRNA amplicon‑based profiling. Both platforms use a container‑based approach to streamline the evaluation process and leverage the ability of many methods to build reference databases. This enables all tools to be compared under identical conditions and using consistent reference data over time. This Zenodo entry provides the source code of the LEMMIv2 shotgun metagenomic pipeline for standalone use to conduct personal benchmarks.Public benchmark results and additional information regarding installation, usage, licensing, and citation can be found on the following website: https://lemmi.ezlab.org/