{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T07:32:10Z","timestamp":1774942330760,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2018,8,16]],"date-time":"2018-08-16T00:00:00Z","timestamp":1534377600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","award":["MRC-RFA-UFSP-01-2013\/UKZN HIVEPI"],"award-info":[{"award-number":["MRC-RFA-UFSP-01-2013\/UKZN HIVEPI"]}],"id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Royal Society Newton Advanced Fellowship"},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Program","award":["634650"],"award-info":[{"award-number":["634650"]}]},{"name":"National Institutes of Health Common Fund","award":["U24HG006941"],"award-info":[{"award-number":["U24HG006941"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. The application uses a novel alignment method that constructs genomes by reference-based linking of de novo contigs by combining amino-acids and nucleotide scores. The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses. User time is minimal and it is limited to the time required to upload the data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Available online: http:\/\/www.genomedetective.com\/app\/typingtool\/virus\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty695","type":"journal-article","created":{"date-parts":[[2018,8,14]],"date-time":"2018-08-14T11:23:00Z","timestamp":1534245780000},"page":"871-873","source":"Crossref","is-referenced-by-count":370,"title":["Genome Detective: an automated system for virus identification from high-throughput sequencing data"],"prefix":"10.1093","volume":"35","author":[{"given":"Michael","family":"Vilsker","sequence":"first","affiliation":[{"name":"Emweb bvba, Herent, Belgium"}]},{"given":"Yumna","family":"Moosa","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"}]},{"given":"Sam","family":"Nooij","sequence":"additional","affiliation":[{"name":"The Dutch National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands"}]},{"given":"Vagner","family":"Fonseca","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"},{"name":"Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil"},{"name":"Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB\/CPqGM\/FIOCRUZ), Bahia, Brazil"}]},{"given":"Yoika","family":"Ghysens","sequence":"additional","affiliation":[{"name":"Emweb bvba, Herent, Belgium"}]},{"given":"Korneel","family":"Dumon","sequence":"additional","affiliation":[{"name":"Emweb bvba, Herent, Belgium"}]},{"given":"Raf","family":"Pauwels","sequence":"additional","affiliation":[{"name":"Emweb bvba, Herent, Belgium"}]},{"given":"Luiz Carlos","family":"Alcantara","sequence":"additional","affiliation":[{"name":"Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil"},{"name":"Laboratory of Hematology Genetic and computational Biology, Goncalo Moniz Research Center, Oswaldo Cruz Foundation (LHGB\/CPqGM\/FIOCRUZ), Bahia, Brazil"},{"name":"Laborat\u00f3rio de Flaviv\u00edrus, IOC, Funda\u00e7\u00e3o Oswaldo Cruz"}]},{"given":"Ewout","family":"Vanden Eynden","sequence":"additional","affiliation":[{"name":"KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium"}]},{"given":"Anne-Mieke","family":"Vandamme","sequence":"additional","affiliation":[{"name":"KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium"},{"name":"Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal"}]},{"given":"Koen","family":"Deforche","sequence":"additional","affiliation":[{"name":"Emweb bvba, Herent, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3027-5254","authenticated-orcid":false,"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, Nelson R Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa"}]}],"member":"286","published-online":{"date-parts":[[2018,8,16]]},"reference":[{"key":"2023060805415236800_bty695-B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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