{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,6]],"date-time":"2025-06-06T04:08:50Z","timestamp":1749182930698,"version":"3.41.0"},"reference-count":12,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T00:00:00Z","timestamp":1749081600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T00:00:00Z","timestamp":1749081600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101081957"],"award-info":[{"award-number":["101081957"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["460129525 (NFDI4Microbiota)"],"award-info":[{"award-number":["460129525 (NFDI4Microbiota)"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Fonden","doi-asserted-by":"publisher","award":["NNF200C0062223"],"award-info":[{"award-number":["NNF200C0062223"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Forschungszentrum J\u00fclich GmbH"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BioData Mining"],"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Publicly available metagenomics datasets are crucial for ensuring the reproducibility of scientific findings and supporting contemporary large-scale studies. However, submitting a comprehensive metagenomics dataset is both cumbersome and time-consuming. It requires including sample information, sequencing reads, assemblies, binned contigs, metagenome-assembled genomes (MAGs), and appropriate metadata. As a result, metagenomics studies are often published with incomplete datasets or, in some cases, without any data at all. subMG addresses this challenge by simplifying and automating the data submission process, thereby encouraging broader and more consistent data sharing.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>subMG streamlines the process of submitting metagenomics study results to the European Nucleotide Archive (ENA) by allowing researchers to input files and metadata from their studies in a single form and automating downstream tasks that otherwise require extensive manual effort and expertise. The tool comes with comprehensive documentation as well as example data tailored for different use cases and can be operated via the command-line or a graphical user interface (GUI), making it easily deployable to a wide range of potential users.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>By simplifying the submission of genome-resolved metagenomics study datasets, subMG significantly reduces the time, effort, and expertise required from researchers, thus paving the way for more numerous and comprehensive data submissions in the future. An increased availability of well-documented and FAIR data can benefit future research, particularly in meta-analyses and comparative studies.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s13040-025-00453-w","type":"journal-article","created":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T16:34:39Z","timestamp":1749141279000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["subMG automates data submission for metagenomics studies"],"prefix":"10.1186","volume":"18","author":[{"given":"Tom","family":"Tubbesing","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Schl\u00fcter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Sczyrba","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,6,5]]},"reference":[{"key":"453_CR1","unstructured":"European Nucleotide Archive. ENA data submission: submitting metagenome assemblies. 2025. https:\/\/ena-docs.readthedocs.io\/en\/latest\/submit\/assembly\/metagenome.html. Accessed 25 Mar 2025."},{"issue":"1","key":"453_CR2","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","volume":"3","author":"MD Wilkinson","year":"2016","unstructured":"Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016;3(1):160018. https:\/\/doi.org\/10.1038\/sdata.2016.18.","journal-title":"Sci Data."},{"issue":"4","key":"453_CR3","doi-asserted-by":"publisher","first-page":"e3000698","DOI":"10.1371\/journal.pbio.3000698","volume":"18","author":"EM Eckert","year":"2020","unstructured":"Eckert EM, Di Cesare A, Fontaneto D, Berendonk TU, B\u00fcrgmann H, Cytryn E, et al. Every fifth published metagenome is not available to science. PLoS Biol. 2020;18(4):e3000698. https:\/\/doi.org\/10.1371\/journal.pbio.3000698.","journal-title":"PLoS Biol."},{"key":"453_CR4","unstructured":"European Nucleotide Archive. Webin command line submission interface (Webin-CLI). 2025. GitHub Repository. https:\/\/github.com\/enasequence\/webin-cli. Accessed 25 Mar 2025."},{"issue":"8","key":"453_CR5","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nbt.3893","volume":"35","author":"RM Bowers","year":"2017","unstructured":"Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35(8):725\u201331. https:\/\/doi.org\/10.1038\/nbt.3893.","journal-title":"Nat Biotechnol."},{"issue":"7","key":"453_CR6","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","volume":"25","author":"DH Parks","year":"2015","unstructured":"Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043\u201355. https:\/\/doi.org\/10.1101\/gr.186072.114.","journal-title":"Genome Res."},{"issue":"6","key":"453_CR7","doi-asserted-by":"publisher","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","volume":"36","author":"PA Chaumeil","year":"2019","unstructured":"Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36(6):1925\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btz848.","journal-title":"Bioinformatics."},{"issue":"1","key":"453_CR8","doi-asserted-by":"publisher","first-page":"e0210347","DOI":"10.1371\/journal.pone.0210347","volume":"14","author":"M Gruenstaeudl","year":"2019","unstructured":"Gruenstaeudl M, Hartmaring Y. EMBL2checklists: a Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA. PLoS ONE. 2019;14(1):e0210347.","journal-title":"PLoS ONE."},{"issue":"1","key":"453_CR9","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1186\/s12859-020-03694-0","volume":"21","author":"M Qui\u00f1ones","year":"2020","unstructured":"Qui\u00f1ones M, Liou DT, Shyu C, Kim W, Vujkovic-Cvijin I, Belkaid Y, et al. METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI\u2019s sequence read archive. BMC Bioinformatics. 2020;21(1):378.","journal-title":"BMC Bioinformatics."},{"key":"453_CR10","unstructured":"Genomic Standards Consortium. Standards Introduction; 2025. Genomic Standards Consortium web page. https:\/\/www.gensc.org\/pages\/standards-intro.html. Accessed 8 May 2025."},{"key":"453_CR11","unstructured":"usegalaxy-eu. ENA upload tool (ENA-upload-CLI); 2025. GitHub Repository. https:\/\/github.com\/usegalaxy-eu\/ena-upload-cli. Accessed 12 May 2025."},{"issue":"18","key":"453_CR12","doi-asserted-by":"publisher","first-page":"2354","DOI":"10.1093\/bioinformatics\/btq415","volume":"26","author":"P Rocca-Serra","year":"2010","unstructured":"Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, et al. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. 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