{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T17:18:01Z","timestamp":1764782281527,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T00:00:00Z","timestamp":1623024000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003130","name":"Fonds Wetenschappelijk Onderzoek","doi-asserted-by":"publisher","award":["I002819N"],"award-info":[{"award-number":["I002819N"]}],"id":[{"id":"10.13039\/501100003130","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sonderforschungsbereich"},{"name":"TRR","award":["167\/2 Z01"],"award-info":[{"award-number":["167\/2 Z01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatics knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CLI ENA upload tool is available at github.com\/usegalaxy-eu\/ena-upload-cli (DOI 10.5281\/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu\/view\/iuc\/ena_upload\/382518f24d6d and github.com\/galaxyproject\/tools-iuc\/tree\/master\/tools\/ena_upload (development); and ENA upload Galaxy container at github.com\/ELIXIR-Belgium\/ena-upload-container (DOI 10.5281\/zenodo.4730785).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab421","type":"journal-article","created":{"date-parts":[[2021,6,5]],"date-time":"2021-06-05T11:23:50Z","timestamp":1622892230000},"page":"3983-3985","source":"Crossref","is-referenced-by-count":4,"title":["A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7461-1427","authenticated-orcid":false,"given":"Miguel","family":"Roncoroni","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3079-6586","authenticated-orcid":false,"given":"Bert","family":"Droesbeke","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Ignacio","family":"Eguinoa","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]},{"given":"Kim","family":"De Ruyck","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]},{"given":"Flora","family":"D\u2019Anna","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]},{"given":"Dilmurat","family":"Yusuf","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , 79110 Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"}]},{"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , 79110 Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"}]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Freiburg , 79110 Freiburg im Breisgau, Baden-W\u00fcrttemberg, Germany"}]},{"given":"Frederik","family":"Coppens","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology , 9052 Ghent, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2021,6,7]]},"reference":[{"key":"2023051607342712200_btab421-B1","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gkaa967","article-title":"The international nucleotide sequence database collaboration","volume":"49","author":"Arita","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023051607342712200_btab421-B2","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/s41591-020-0935-z","article-title":"Ten recommendations for supporting open pathogen genomic analysis in public health","volume":"26","author":"Black","year":"2020","journal-title":"Nat. Med"},{"key":"2023051607342712200_btab421-B3","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"Li","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051607342712200_btab421-B4","article-title":"Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring","author":"Maier","year":"2021","journal-title":"bioRXiv"},{"key":"2023051607342712200_btab421-B5","doi-asserted-by":"crossref","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"2023051607342712200_btab421-B6","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab421\/38843742\/btab421.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/21\/3983\/50336649\/btab421.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/21\/3983\/50336649\/btab421.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T08:00:59Z","timestamp":1684224059000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/21\/3983\/6294398"}},"subtitle":[],"editor":[{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,6,7]]},"references-count":6,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2021,11,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab421","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,11,1]]},"published":{"date-parts":[[2021,6,7]]}}}