{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T04:10:40Z","timestamp":1779336640443,"version":"3.51.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Paris \u00cele-de-France Region"},{"name":"French ANR"},{"name":"JEMINI","award":["ANR-24-PESA-0010"],"award-info":[{"award-number":["ANR-24-PESA-0010"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>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\u2014quality control, assembly, binning, dereplication, taxonomic and functional annotation\u2014while 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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\u2019s benchmarking capacity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>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).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag212","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:28:48Z","timestamp":1777980528000},"source":"Crossref","is-referenced-by-count":0,"title":["StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-5945-9359","authenticated-orcid":false,"given":"Baptiste","family":"Hennecart","sequence":"first","affiliation":[{"name":"IRD, Sorbonne Universit\u00e9, UMMISCO , Paris, 75005,","place":["France"]},{"name":"GMT Science , Paris, 75013,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4307-5072","authenticated-orcid":false,"given":"Eugeni","family":"Belda","sequence":"additional","affiliation":[{"name":"IRD, Sorbonne Universit\u00e9, UMMISCO , Paris, 75005,","place":["France"]},{"name":"Sorbonne University, INSERM, nutrition and obesities: systemic approaches, NutriOmique , Paris, 75013,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2862-9589","authenticated-orcid":false,"given":"Raynald","family":"de Lahond\u00e8s","sequence":"additional","affiliation":[{"name":"GMT Science , Paris, 75013,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5597-7922","authenticated-orcid":false,"given":"Jean-Daniel","family":"Zucker","sequence":"additional","affiliation":[{"name":"IRD, Sorbonne Universit\u00e9, UMMISCO , Paris, 75005,","place":["France"]},{"name":"Sorbonne University, INSERM, nutrition and obesities: systemic approaches, NutriOmique , Paris, 75013,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8861-1305","authenticated-orcid":false,"given":"Edi","family":"Prifti","sequence":"additional","affiliation":[{"name":"IRD, Sorbonne Universit\u00e9, UMMISCO , Paris, 75005,","place":["France"]},{"name":"Sorbonne University, INSERM, nutrition and obesities: systemic approaches, NutriOmique , Paris, 75013,","place":["France"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"2026052023565179700_btag212-B1","doi-asserted-by":"publisher","first-page":"1071","DOI":"10.1089\/cmb.2017.0013","article-title":"U50: a new metric for measuring assembly output based on non-overlapping, target-specific contigs","volume":"24","author":"Castro","year":"2017","journal-title":"J Comput Biol"},{"key":"2026052023565179700_btag212-B2","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2026052023565179700_btag212-B3","volume-title":"CAMI 2 \u2013 Challenge Datasets","author":"Fritz","year":"2021"},{"key":"2026052023565179700_btag212-B4","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1099\/mic.0.001469","article-title":"Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities","volume":"170","author":"Goussarov","year":"2024","journal-title":"Microbiology (Reading)"},{"key":"2026052023565179700_btag212-B5","doi-asserted-by":"publisher","first-page":"8665","DOI":"10.1038\/s41467-024-52907-0","article-title":"HyLight: strain aware assembly of low coverage metagenomes","volume":"15","author":"Kang","year":"2024","journal-title":"Nat Commun"},{"key":"2026052023565179700_btag212-B6","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s12859-020-03585-4","article-title":"ATLAS: a snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data","volume":"21","author":"Kieser","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2026052023565179700_btag212-B7","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1038\/s12276-024-01262-7","article-title":"Genome-resolved metagenomics: a game changer for microbiome medicine","volume":"56","author":"Kim","year":"2024","journal-title":"Exp Mol Med"},{"key":"2026052023565179700_btag212-B8","doi-asserted-by":"publisher","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with snakemake","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res"},{"key":"2026052023565179700_btag212-B9","author":"Newell","year":"2024"},{"key":"2026052023565179700_btag212-B10","doi-asserted-by":"publisher","first-page":"727","DOI":"10.1038\/s41587-020-00797-0","article-title":"inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains","volume":"39","author":"Olm","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2026052023565179700_btag212-B11","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1007\/978-1-0716-3838-5_6","volume-title":"Comparative Genomics","author":"Sanchez","year":"2024"},{"key":"2026052023565179700_btag212-B12","doi-asserted-by":"publisher","first-page":"i30","DOI":"10.1093\/bioinformatics\/btae252","article-title":"Floria: fast and accurate strain haplotyping in metagenomes","volume":"40","author":"Shaw","year":"2024","journal-title":"Bioinformatics"},{"key":"2026052023565179700_btag212-B13","doi-asserted-by":"publisher","first-page":"3349","DOI":"10.3389\/fmicb.2018.03349","article-title":"SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline","volume":"9","author":"Tamames","year":"2018","journal-title":"Front Microbiol"},{"key":"2026052023565179700_btag212-B14","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"2026052023565179700_btag212-B15","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/s41579-020-0368-1","article-title":"Diversity within species: interpreting strains in microbiomes","volume":"18","author":"Van Rossum","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"2026052023565179700_btag212-B16","doi-asserted-by":"publisher","first-page":"6301","DOI":"10.1016\/j.csbj.2021.11.028","article-title":"A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data","volume":"19","author":"Yang","year":"2021","journal-title":"Comput Struct Biotechnol J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag212\/68246583\/btag212.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/5\/btag212\/68246583\/btag212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/5\/btag212\/68246583\/btag212.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T03:57:09Z","timestamp":1779335829000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag212\/8672507"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":16,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,5,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag212","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,5]]},"published":{"date-parts":[[2026,5]]},"article-number":"btag212"}}