{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T06:38:55Z","timestamp":1784097535405,"version":"3.55.0"},"reference-count":18,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100006489","name":"Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006489","id-type":"DOI","asserted-by":"publisher"}]},{"name":"France G\u00e9nomique"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>One of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of real-time sequencing. This gives access to information during the experiment and allows either to control the sequencing or to stop the sequencing once the results have been obtained. However, the ONT sequencing interface is not sufficient to explore the quality of sequencing data in depth and existing quality control tools do not take full advantage of real-time data streaming.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Herein, we present BoardION, an interactive web application to analyze the efficiency of ONT sequencing runs. The interactive interface of BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the data generated during the experiment. It also enables the comparison of multiple flowcells to assess library preparation protocols or the quality of input samples.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      BoardION is dedicated to people who manage ONT sequencing instruments and allows them to remotely and in real time monitor their experiments and compare multiple sequencing runs. Source code, a Docker image and a demo version are available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.genoscope.cns.fr\/boardion\/\">http:\/\/www.genoscope.cns.fr\/boardion\/<\/jats:ext-link>\n                      <jats:underline>.<\/jats:underline>\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-021-04161-0","type":"journal-article","created":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T08:02:31Z","timestamp":1620892951000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["BoardION: real-time monitoring of Oxford Nanopore sequencing instruments"],"prefix":"10.1186","volume":"22","author":[{"given":"Aimeric","family":"Bruno","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Marc","family":"Aury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0003-1192","authenticated-orcid":false,"given":"Stefan","family":"Engelen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,13]]},"reference":[{"key":"4161_CR1","doi-asserted-by":"publisher","first-page":"10931","DOI":"10.1038\/s41598-018-29334-5","volume":"8","author":"AD Tyler","year":"2018","unstructured":"Tyler AD, et al. Evaluation of Oxford Nanopore\u2019s minion sequencing device for microbial whole genome sequencing applications. Sci Rep. 2018;8:10931.","journal-title":"Sci Rep"},{"key":"4161_CR2","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","volume":"17","author":"M Jain","year":"2016","unstructured":"Jain M, et al. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016;17:239.","journal-title":"Genome Biol"},{"key":"4161_CR3","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nbt.4060","volume":"36","author":"M Jain","year":"2018","unstructured":"Jain M, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338\u201345.","journal-title":"Nat Biotechnol"},{"key":"4161_CR4","doi-asserted-by":"publisher","first-page":"12608","DOI":"10.1111\/dgd.12608","volume":"61","author":"N Kono","year":"2019","unstructured":"Kono N, et al. Nanopore sequencing: review of potential applications in functional genomics. Dev Growth Differ. 2019;61:12608.","journal-title":"Dev Growth Differ"},{"issue":"12","key":"4161_CR5","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1093\/gigascience\/giaa137","volume":"9","author":"M Rousseau-Gueutin","year":"2020","unstructured":"Rousseau-Gueutin M, et al. Long-read assembly of the Brassica napus reference genome Darmor-bzh. GigaScience. 2020;9(12):137.","journal-title":"GigaScience"},{"key":"4161_CR6","doi-asserted-by":"publisher","first-page":"14908","DOI":"10.1038\/s41598-019-51470-9","volume":"9","author":"C Sessegolo","year":"2019","unstructured":"Sessegolo C, et al. Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules. Sci Rep. 2019;9:14908.","journal-title":"Sci Rep"},{"key":"4161_CR7","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nmeth.4184","volume":"14","author":"JT Simpson","year":"2017","unstructured":"Simpson JT, et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017;14:407\u201310.","journal-title":"Nat Methods"},{"key":"4161_CR8","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01315-19","author":"LM Petersen","year":"2019","unstructured":"Petersen LM, et al. Third generation sequencing in the clinical laboratory: exploring the advantages and 2 challenges of nanopore sequencing. J Clin Microbiol. 2019. https:\/\/doi.org\/10.1128\/JCM.01315-19.","journal-title":"J Clin Microbiol"},{"key":"4161_CR9","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1007\/s00401-017-1743-5","volume":"134","author":"P Euskirchen","year":"2017","unstructured":"Euskirchen P, et al. Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing. Acta Neuropathol. 2017;134:691\u2013703.","journal-title":"Acta Neuropathol"},{"issue":"3","key":"4161_CR10","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1093\/bioinformatics\/bty654","volume":"35","author":"R Lanfear","year":"2019","unstructured":"Lanfear R, et al. MinIONQC: fast and simple quality control for MinION sequencing data. Bioinformatics. 2019;35(3):523\u20135.","journal-title":"Bioinformatics"},{"issue":"34","key":"4161_CR11","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.21105\/joss.01236","volume":"4","author":"A Leger","year":"2019","unstructured":"Leger A, et al. pycoQC, interactive quality control for Oxford Nanopore Sequencing. J Open Source Softw. 2019;4(34):1236.","journal-title":"J Open Source Softw"},{"issue":"15","key":"4161_CR12","doi-asserted-by":"publisher","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","volume":"34","author":"W De Coster","year":"2018","unstructured":"De Coster W, et al. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018;34(15):2666\u20139.","journal-title":"Bioinformatics"},{"key":"4161_CR13","unstructured":"Laffay B, et al. ToulligQC: a post sequencing QC tool for Oxford Nanopore sequencers. Github. https:\/\/github.com\/GenomicParisCentre\/toulligQC. Accessed 10 Jan 2020."},{"key":"4161_CR14","unstructured":"Loose M. minoTour: Real time data analysis tools for the MinION sequencing platform. Github; 2015. https:\/\/github.com\/minoTour\/minoTour. Accessed 1 Oct 2020."},{"key":"4161_CR15","unstructured":"Chang W, et al. Shiny: web application framework for R. R package version 1.4.0. 2019. https:\/\/CRAN.R-project.org\/package=shiny."},{"key":"4161_CR16","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: elegant graphics for data analysis","author":"H Wickham","year":"2009","unstructured":"Wickham H. ggplot2: elegant graphics for data analysis. Springer; 2009."},{"key":"4161_CR17","unstructured":"Sievert C. plotly for R. 2018. https:\/\/plotly-r.com."},{"key":"4161_CR18","unstructured":"Oxford Nanopore Technologies. Refuelling a sequencing run. 2019. https:\/\/community.nanoporetech.com\/posts\/refuelling-a-sequencing-ru. Accessed 11 Mar 2020."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04161-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-021-04161-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-021-04161-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T08:02:57Z","timestamp":1620892977000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-021-04161-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,13]]},"references-count":18,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["4161"],"URL":"https:\/\/doi.org\/10.1186\/s12859-021-04161-0","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.06.09.142273","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,13]]},"assertion":[{"value":"5 January 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests. J.-M.A. received travel and accommodation expenses to speak at ONT conferences.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"245"}}