%0 Journal Article
%9 ACL : Articles dans des revues avec comité de lecture répertoriées par l'AERES
%A Hennecart, Baptiste
%A Belda, E.
%A de Lahondès, R.
%A Zucker, Jean-Daniel
%A Prifti, Edi
%T StrainMake : reproducible hybrid metagenomics with MAG recovery and strain-level resolution
%D 2026
%L fdi:010097131
%G ENG
%J Bioinformatics
%@ 1367-4803
%M ISI:001769592300001
%N 5
%P btag212 [4 ]
%R 10.1093/bioinformatics/btag212
%U https://www.documentation.ird.fr/hor/fdi:010097131
%> https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2026-06/010097131.pdf
%V 42
%W Horizon (IRD)
%X 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).
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