LEMMIv2: Benchmarking Framework for Metagenomic and 16S Amplicon Profilers with a Catalogue of Evaluated Tools

LEMMIv2: Benchmarking Framework for Metagenomic and 16S Amplicon Profilers with a Catalogue of Evaluated Tools | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Method Article LEMMIv2: Benchmarking Framework for Metagenomic and 16S Amplicon Profilers with a Catalogue of Evaluated Tools Mathieu Seppey, Andres Benavides, Matthew R. Berkeley, Mosè Manni, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6999366/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 28 Apr, 2026 Read the published version in Genome Biology → Version 1 posted 9 You are reading this latest preprint version Abstract Metagenomics has enabled the study of microbial communities without the need for culturing or prior knowledge of sample composition. However, the analysis of the sequencing reads is complex and has led to a multitude of computational strategies, the choice of which poses a challenge for practitioners and creates visibility barriers for novel tools. Here, we present LEMMI v2 ( https://lemmi.ezlab.org ), a major evolution of our platform for continuous benchmarking of metagenomic profilers, where developers can receive impartial benchmarks and users benefit from a catalogue of evaluated tools. We also extend the approach to 16S amplicon profiling with LEMMI16S ( https://www.lemmi16s.ezlab.org ). Full Text Additional Declarations No competing interests reported. Supplementary Files LEMMIv216sSupplementary.docx Cite Share Download PDF Status: Published Journal Publication published 28 Apr, 2026 Read the published version in Genome Biology → Version 1 posted Editorial decision: Revision requested 11 Sep, 2025 Reviews received at journal 23 Aug, 2025 Reviews received at journal 22 Aug, 2025 Reviewers agreed at journal 28 Jul, 2025 Reviewers agreed at journal 25 Jul, 2025 Reviewers invited by journal 16 Jul, 2025 Editor assigned by journal 30 Jun, 2025 Submission checks completed at journal 30 Jun, 2025 First submitted to journal 28 Jun, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6999366","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Method Article","associatedPublications":[],"authors":[{"id":486404255,"identity":"1ff27054-bcec-4f20-8d98-cdfd68597e23","order_by":0,"name":"Mathieu Seppey","email":"","orcid":"","institution":"University of Geneva Medical School and Swiss Institute of Bioinformatics","correspondingAuthor":false,"prefix":"","firstName":"Mathieu","middleName":"","lastName":"Seppey","suffix":""},{"id":486404256,"identity":"4033c63d-3221-4bd5-abe9-0b003db80216","order_by":1,"name":"Andres Benavides","email":"","orcid":"","institution":"University of Geneva Medical School and Swiss Institute of Bioinformatics","correspondingAuthor":false,"prefix":"","firstName":"Andres","middleName":"","lastName":"Benavides","suffix":""},{"id":486404257,"identity":"bbe48f50-d20a-485a-b68e-b17899cac8c4","order_by":2,"name":"Matthew R. 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