{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T11:04:03Z","timestamp":1792494243089,"version":"4.5.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,1,24]],"date-time":"2025-01-24T00:00:00Z","timestamp":1737676800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,2,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator\u2014a comprehensive, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and noncoding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarizes these results in a GFF (General Feature Format) file that can be easily utilized in downstream analysis or visualized using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel metagenome-assembled genomes, and present metrics on its performance in comparison to other tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https:\/\/github.com\/EBI-Metagenomics\/mettannotator. The pipeline is also available on WorkflowHub: https:\/\/workflowhub.eu\/workflows\/1069.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf037","type":"journal-article","created":{"date-parts":[[2025,1,22]],"date-time":"2025-01-22T07:15:03Z","timestamp":1737530103000},"source":"Crossref","is-referenced-by-count":11,"title":["mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7537-8871","authenticated-orcid":false,"given":"Tatiana A","family":"Gurbich","sequence":"first","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Beracochea","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4802-2375","authenticated-orcid":false,"given":"Nishadi H","family":"De Silva","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8626-2148","authenticated-orcid":false,"given":"Robert D","family":"Finn","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Cambridge CB10 1SD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,24]]},"reference":[{"key":"2025030422261354000_btaf037-B1","doi-asserted-by":"publisher","first-page":"D693","DOI":"10.1093\/nar\/gkab1016","article-title":"Rhea, the reaction knowledgebase in 2022","volume":"50","author":"Bansal","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025030422261354000_btaf037-B2","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","author":"Bateman","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025030422261354000_btaf037-B3","doi-asserted-by":"publisher","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-Mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic 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