Hennecart Baptiste auteur aut IRD Belda E. auteur aut IRD de Lahondès R. auteur aut IRD Zucker Jean-Daniel auteur aut IRD Prifti Edi auteur aut IRD text journalArticle eng text/pdf reformatted digital access 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). specialized 020 122 42 5 btag212 [4 p.] 2026 1367-4803 https://www.documentation.ird.fr/hor/fdi:010097131 10.1093/bioinformatics/btag212 1367-4803 [F B010097131] https://www.documentation.ird.fr/hor/fdi:010097131 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2026-06/010097131.pdf IRD - Base Horizon / Pleins textes 2026-06-10 2026-06-10 fdi:010097131 fre