{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T23:20:12Z","timestamp":1771456812029,"version":"3.50.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,5]],"date-time":"2019-04-05T00:00:00Z","timestamp":1554422400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AIRC Investigator","award":["20307"],"award-info":[{"award-number":["20307"]}]},{"name":"Third Generation Cancer Genomics","award":["#21267"],"award-info":[{"award-number":["#21267"]}]},{"name":"MYeloid NEoplasms Research Venture AIRC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION\/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6\u201312\u00a0h allow to obtain a resolution comparable to currently available array-based technologies, and thanks to a novel probabilistic approach are capable to predict the allelic fraction of genomic alteration with high accuracy. To exploit the unique characteristics of nanopore sequencing data we developed a novel software tool, Nano-GLADIATOR, that is capable to perform copy number variants\/alterations detection and allelic fraction prediction during the sequencing run (\u2018On-line\u2019 mode) and after experiment completion (\u2018Off-line\u2019 mode). We tested Nano-GLADIATOR on publicly available (\u2018Off-line\u2019 mode) and on novel whole genome sequencing dataset generated with MinION device (\u2018On-line\u2019 mode) showing that our tool is capable to perform real-time copy number alterations detection obtaining good results with respect to other state-of-the-art tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Nano-GLADIATOR is freely available at https:\/\/sourceforge.net\/projects\/nanogladiator\/.<\/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\/btz241","type":"journal-article","created":{"date-parts":[[2019,4,3]],"date-time":"2019-04-03T13:33:20Z","timestamp":1554298400000},"page":"4213-4221","source":"Crossref","is-referenced-by-count":21,"title":["Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data"],"prefix":"10.1093","volume":"35","author":[{"given":"Alberto","family":"Magi","sequence":"first","affiliation":[{"name":"Department of Information Engineering, University of Florence , Florence, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8735-8093","authenticated-orcid":false,"given":"Davide","family":"Bolognini","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, University of Florence , Florence, Italy"}]},{"given":"Niccol\u00f3","family":"Bartalucci","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, CRIMM, Center Research and Innovation of Myeloproliferative Neoplasms, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy"}]},{"given":"Alessandra","family":"Mingrino","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, University of Florence , Florence, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0601-6903","authenticated-orcid":false,"given":"Roberto","family":"Semeraro","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, University of Florence , Florence, Italy"}]},{"given":"Luna","family":"Giovannini","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, University of Florence , Florence, Italy"}]},{"given":"Stefania","family":"Bonifacio","sequence":"additional","affiliation":[{"name":"Department of Laboratory Diagnosis, Genetic Diagnosis Service, Careggi Teaching Hospital , Florence, Italy"}]},{"given":"Daniela","family":"Parrini","sequence":"additional","affiliation":[{"name":"Department of Laboratory Diagnosis, Genetic Diagnosis Service, Careggi Teaching Hospital , Florence, Italy"}]},{"given":"Elisabetta","family":"Pelo","sequence":"additional","affiliation":[{"name":"Department of Laboratory Diagnosis, Genetic Diagnosis Service, Careggi Teaching Hospital , Florence, Italy"}]},{"given":"Francesco","family":"Mannelli","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, CRIMM, Center Research and Innovation of Myeloproliferative Neoplasms, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy"}]},{"given":"Paola","family":"Guglielmelli","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, CRIMM, Center Research and Innovation of Myeloproliferative Neoplasms, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy"}]},{"given":"Alessandro","family":"Maria Vannucchi","sequence":"additional","affiliation":[{"name":"Department of Experimental and Clinical Medicine, CRIMM, Center Research and Innovation of Myeloproliferative Neoplasms, Azienda Ospedaliera Universitaria Careggi, University of Florence , Florence, Italy"}]}],"member":"286","published-online":{"date-parts":[[2019,4,5]]},"reference":[{"key":"2023062712454626100_btz241-B1","doi-asserted-by":"crossref","first-page":"363.","DOI":"10.1038\/nrg2958","article-title":"Genome structural variation discovery and genotyping","volume":"12","author":"Alkan","year":"2011","journal-title":"Nat. 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