{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,27]],"date-time":"2025-09-27T00:11:56Z","timestamp":1758931916210,"version":"3.44.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T00:00:00Z","timestamp":1757894400000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009708","name":"The Novo Nordisk Foundation","doi-asserted-by":"crossref","award":["0054575-SuPAcow"],"award-info":[{"award-number":["0054575-SuPAcow"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation programme","award":["101000213"],"award-info":[{"award-number":["101000213"]}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["FT230100560"],"award-info":[{"award-number":["FT230100560"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, designed in such a way that the user can install the complete software in one step and launch all analyses on a set of microbial genomes (bacterial and archaeal) in a single action. The central results generated via the CompareM2 workflow are emphasized in a portable dynamic report document.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CompareM2 is a free software that is scalable to a range of project sizes, and welcomes modifications and pull requests from the community on its Git repository at https:\/\/github.com\/cmkobel\/comparem2.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf517","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T20:16:38Z","timestamp":1758312998000},"source":"Crossref","is-referenced-by-count":0,"title":["CompareM2 is a genomes-to-report pipeline for comparing microbial genomes"],"prefix":"10.1093","volume":"41","author":[{"given":"Carl M","family":"Kobel","sequence":"first","affiliation":[{"name":"Faculty of Biosciences, Norwegian University of Life Sciences , \u00c5s,","place":["Norway"]}]},{"given":"Velma T E","family":"Aho","sequence":"additional","affiliation":[{"name":"Faculty of Biosciences, Norwegian University of Life Sciences , \u00c5s,","place":["Norway"]}]},{"given":"Ove","family":"\u00d8y\u00e5s","sequence":"additional","affiliation":[{"name":"Faculty of Biosciences, Norwegian University of Life Sciences , \u00c5s,","place":["Norway"]}]},{"given":"Niels","family":"N\u00f8rskov-Lauritsen","sequence":"additional","affiliation":[{"name":"Clinical Institute, University of Southern Denmark , Odense,","place":["Denmark"]}]},{"given":"Ben J","family":"Woodcroft","sequence":"additional","affiliation":[{"name":"Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute , Woolloongabba,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2067-4059","authenticated-orcid":false,"given":"Phillip 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