{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T19:16:25Z","timestamp":1771355785533,"version":"3.50.1"},"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T00:00:00Z","timestamp":1771286400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-11-INBS-0013"],"award-info":[{"award-number":["ANR-11-INBS-0013"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Federal Ministry of Education and Research","award":["031 A538A de.NBI-RBC"],"award-info":[{"award-number":["031 A538A de.NBI-RBC"]}]},{"name":"Ministry of Science, Research and the Arts Baden-W\u00c3\u00bcrttemberg"},{"name":"European Union\u00e2\u20ac\u2122s Horizon Europe programme","award":["HORIZON-INFRA-2021-EOSC-01-04 (101057388)"],"award-info":[{"award-number":["HORIZON-INFRA-2021-EOSC-01-04 (101057388)"]}]},{"name":"REA.B.3, Biodiversity, Circular Economy and Environment","award":["BGE 101059492"],"award-info":[{"award-number":["BGE 101059492"]}]},{"DOI":"10.13039\/100000002","name":"U.S. National Institutes of Health","doi-asserted-by":"crossref","award":["U24HG006620, U24HG010263, U24AI183870, U24CA284167, and OT2OD037936"],"award-info":[{"award-number":["U24HG006620, U24HG010263, U24AI183870, U24CA284167, and OT2OD037936"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["2419522"],"award-info":[{"award-number":["2419522"]}]},{"name":"European Commission\u00e2\u20ac\u2122s Horizon Europe Research and Innovation programme","award":["101129751"],"award-info":[{"award-number":["101129751"]}]},{"name":"European Union\u00e2\u20ac\u2122s Horizon 2020 research and innovation program","award":["No 857560 (CETOCOEN Excellence),"],"award-info":[{"award-number":["No 857560 (CETOCOEN Excellence),"]}]},{"name":"Programme Johannes Amos Comenius under the Ministry of Education, Youth and Sports (MEYS) - Co-funded by the European Union","award":["grant SALVAGE (CZ.02.01.01\/00\/22_008\/0004644)"],"award-info":[{"award-number":["grant SALVAGE (CZ.02.01.01\/00\/22_008\/0004644)"]}]},{"name":"MEYS","award":["RECETOX RI (LM2023069)"],"award-info":[{"award-number":["RECETOX RI (LM2023069)"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Galaxy is a widely used open-source platform for accessible, reproducible, transparent and scalable data analysis in the life sciences and beyond. Despite its growing adoption across domains, several misconceptions persist about its scope, usability, scalability and relevance to academia and industry. In this manuscript, we identify and address 10 common misconceptions about Galaxy, ranging from the belief that it is limited to genomics, lacks scalability, or is only useful for teaching, to doubts about its ability to support secure data analysis or maintain high software quality as a free and open-source project. We refute each misconception with present evidence based on Galaxy\u2019s technical features, real-world use cases, user communities and governance structures. We show that Galaxy is a mature and versatile platform capable of supporting cutting-edge scientific research, education and even clinical workflows across a wide variety of disciplines. By clarifying existing misconceptions, we aim to help researchers, educators, developers and decision-makers better appreciate Galaxy\u2019s capabilities and potential within their fields.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013869","type":"journal-article","created":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T18:31:25Z","timestamp":1771353085000},"page":"e1013869","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ten common misconceptions about Galaxy (and why they are wrong!)"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8170-8806","authenticated-orcid":true,"given":"Wendi Anne","family":"Bacon","sequence":"first","affiliation":[]},{"given":"B\u00e9r\u00e9nice","family":"Batut","sequence":"additional","affiliation":[]},{"given":"Sanjay Kumar","family":"Srikakulam","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Zierep","sequence":"additional","affiliation":[]},{"given":"Anthony","family":"Bretaudeau","sequence":"additional","affiliation":[]},{"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[]},{"given":"Gildas","family":"Le Corguill\u00e9","sequence":"additional","affiliation":[]},{"given":"Helge","family":"Hecht","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1363-1245","authenticated-orcid":true,"given":"John Y.","family":"Davis","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2799-424X","authenticated-orcid":true,"given":"Hans-Rudolf","family":"Hotz","sequence":"additional","affiliation":[]},{"given":"Beatriz","family":"Serrano-Solano","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2026,2,17]]},"reference":[{"issue":"10","key":"pcbi.1013869.ref001","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: A platform for interactive large-scale genome analysis","volume":"15","author":"B Giardine","year":"2005","journal-title":"Genome Res"},{"issue":"6","key":"pcbi.1013869.ref002","article-title":"Community-driven data analysis training for biology","volume":"6","author":"B Batut","year":"2018","journal-title":"Cell Syst"},{"key":"pcbi.1013869.ref003","article-title":"Galaxy: A web-based genome analysis tool for experimentalists","author":"D Blankenberg","year":"2010","journal-title":"Curr Protoc Mol Biol"},{"key":"pcbi.1013869.ref004","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkae410","article-title":"The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update","volume":"52","author":"The Galaxy Community","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"pcbi.1013869.ref005","article-title":"Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine","volume":"17","author":"Q Gu","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1013869.ref006","article-title":"Community-Curated Galaxy Interfaces with the Galaxy Labs Engine [preprint]","author":"CJ Hyde","year":"2025","journal-title":"Preprints.org"},{"issue":"11","key":"pcbi.1013869.ref007","doi-asserted-by":"crossref","DOI":"10.1080\/14789450.2023.2265062","article-title":"A Galaxy of informatics resources for MS-based proteomics","volume":"20","author":"S Mehta","year":"2023","journal-title":"Expert Rev Proteom"},{"key":"pcbi.1013869.ref008","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giae107","article-title":"Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq","volume":"14","author":"CL Goclowski","year":"2025","journal-title":"Gigascience"},{"issue":"9","key":"pcbi.1013869.ref009","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1093\/bioinformatics\/btu813","article-title":"Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics","volume":"31","author":"F Giacomoni","year":"2015","journal-title":"Bioinformatics"},{"issue":"8","key":"pcbi.1013869.ref010","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1002\/job.2199","article-title":"Assessing the not-invented-here syndrome: Development and validation of implicit and explicit measurements","volume":"38","author":"D Antons","year":"2017","journal-title":"J Organiz Behav"},{"key":"pcbi.1013869.ref011","article-title":"An ecosystem of services for FAIR computational workflows [Internet]","author":"SR Wilkinson","year":"2025"},{"issue":"10","key":"pcbi.1013869.ref012","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1038\/s41592-021-01254-9","article-title":"Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers","volume":"18","author":"L Wratten","year":"2021","journal-title":"Nature Methods"},{"key":"pcbi.1013869.ref013","unstructured":"van den Beek M. 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