StrainMake : reproducible hybrid metagenomics with MAG recovery and strain-level resolution /Hennecart, Baptiste Belda, E. de Lahondès, R. /Zucker, Jean-Daniel /Prifti, Edi Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda.Results Applied to the CAMI II strain-madness dataset, StrainMake produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity. Availability and implementation StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi: 10.5281/zenodo.16950162). 2026 text https://www.documentation.ird.fr/hor/fdi:010097131 fdi:010097131 Hennecart Baptiste, Belda E., de Lahondès R., Zucker Jean-Daniel, Prifti Edi. StrainMake : reproducible hybrid metagenomics with MAG recovery and strain-level resolution. 2026, 42 (5), btag212 [4 p.] EN