{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T11:51:25Z","timestamp":1773229885400,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T00:00:00Z","timestamp":1588723200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["872539"],"award-info":[{"award-number":["872539"]}]},{"DOI":"10.13039\/501100005357","name":"Slovak Research and Development Agency","doi-asserted-by":"publisher","award":["APVV-18-0239"],"award-info":[{"award-number":["APVV-18-0239"]}],"id":[{"id":"10.13039\/501100005357","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006109","name":"VEGA","doi-asserted-by":"publisher","award":["1\/0458\/18"],"award-info":[{"award-number":["1\/0458\/18"]}],"id":[{"id":"10.13039\/501100006109","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006109","name":"VEGA","doi-asserted-by":"publisher","award":["1\/0463\/20"],"award-info":[{"award-number":["1\/0463\/20"]}],"id":[{"id":"10.13039\/501100006109","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human\u2013pathogen runs).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https:\/\/github.com\/fmfi-compbio\/deepnano-blitz.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>vladimir.boza@fmph.uniba.sk<\/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\/btaa297","type":"journal-article","created":{"date-parts":[[2020,4,28]],"date-time":"2020-04-28T07:09:43Z","timestamp":1588057783000},"page":"4191-4192","source":"Crossref","is-referenced-by-count":27,"title":["DeepNano-blitz: a fast base caller for MinION nanopore sequencers"],"prefix":"10.1093","volume":"36","author":[{"given":"Vladim\u00edr","family":"Bo\u017ea","sequence":"first","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynsk\u00e1 dolina , Bratislava, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Pere\u0161\u00edni","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynsk\u00e1 dolina , Bratislava, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bro\u0148a","family":"Brejov\u00e1","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynsk\u00e1 dolina , Bratislava, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom\u00e1\u0161","family":"Vina\u0159","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynsk\u00e1 dolina , Bratislava, Slovakia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,6]]},"reference":[{"key":"2023062213541852300_btaa297-B1","doi-asserted-by":"crossref","first-page":"e0178751","DOI":"10.1371\/journal.pone.0178751","article-title":"DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads","volume":"12","author":"Bo\u017ea","year":"2017","journal-title":"PLoS One"},{"key":"2023062213541852300_btaa297-B2","author":"Edwards","year":"2016"},{"key":"2023062213541852300_btaa297-B3","first-page":"369","author":"Graves","year":"2006"},{"key":"2023062213541852300_btaa297-B4","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nbt.4060","article-title":"Nanopore sequencing and assembly of a human genome with ultra-long reads","volume":"36","author":"Jain","year":"2018","journal-title":"Nat. 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