{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T19:44:54Z","timestamp":1775850294722,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T00:00:00Z","timestamp":1627344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Slovak Research Grant Agency","award":["1\/0458\/18"],"award-info":[{"award-number":["1\/0458\/18"]}]},{"name":"Slovak Research Grant Agency","award":["1\/0463\/20"],"award-info":[{"award-number":["1\/0463\/20"]}]},{"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"}]},{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["872539"],"award-info":[{"award-number":["872539"]}]},{"name":"Google Cloud"},{"name":"NVIDIA Corporation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MinION is a portable nanopore sequencing device that can be easily operated in the field with features including monitoring of run progress and selective sequencing. To fully exploit these features, real-time base calling is required. Up to date, this has only been achieved at the cost of high computing requirements that pose limitations in terms of hardware availability in common laptops and energy consumption.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed a new base caller DeepNano-coral for nanopore sequencing, which is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-attached hardware accelerator. To achieve this goal, we have designed new versions of two key components used in convolutional neural networks for speech recognition and base calling. In our components, we propose a new way of factorization of a full convolution into smaller operations, which decreases memory access operations, memory access being a bottleneck on this device. DeepNano-coral achieves real-time base calling during sequencing with the accuracy slightly better than the fast mode of the Guppy base caller and is extremely energy efficient, using only 10\u2009W of power.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/fmfi-compbio\/coral-basecaller<\/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\/btab528","type":"journal-article","created":{"date-parts":[[2021,7,25]],"date-time":"2021-07-25T19:06:50Z","timestamp":1627240010000},"page":"4661-4667","source":"Crossref","is-referenced-by-count":48,"title":["Nanopore base calling on the edge"],"prefix":"10.1093","volume":"37","author":[{"given":"Peter","family":"Pere\u0161\u00edni","sequence":"first","affiliation":[{"name":"Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava , Mlynska dolina, 842 48 Bratislava, Slovakia"}]},{"given":"Vladim\u00edr","family":"Bo\u017ea","sequence":"additional","affiliation":[{"name":"Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava , Mlynska dolina, 842 48 Bratislava, Slovakia"}]},{"given":"Bro\u0148a","family":"Brejov\u00e1","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava , Mlynska dolina, 842 48 Bratislava, Slovakia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3898-3447","authenticated-orcid":false,"given":"Tom\u00e1\u0161","family":"Vina\u0159","sequence":"additional","affiliation":[{"name":"Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava , Mlynska dolina, 842 48 Bratislava, Slovakia"}]}],"member":"286","published-online":{"date-parts":[[2021,7,27]]},"reference":[{"key":"2023051607132057700_btab528-B1","doi-asserted-by":"crossref","first-page":"5282","DOI":"10.1093\/bioinformatics\/btaa1015","article-title":"SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs","volume":"36","author":"Alser","year":"2021","journal-title":"Bioinformatics"},{"key":"2023051607132057700_btab528-B2","doi-asserted-by":"crossref","first-page":"4191","DOI":"10.1093\/bioinformatics\/btaa297","article-title":"DeepNano-blitz: a fast base caller for MinION nanopore sequencers","volume":"36","author":"Boza","year":"2020","journal-title":"Bioinformatics"},{"key":"2023051607132057700_btab528-B3","first-page":"951","author":"Cali","year":"2020"},{"key":"2023051607132057700_btab528-B4","first-page":"69","author":"Fujiki","year":"2018"},{"key":"2023051607132057700_btab528-B5","first-page":"249","volume-title":"Proceedings of the 13th International Conference on Artificial Intelligence and Statistics (AISTATS), Vol. 9 of JMLR Proceedings","author":"Glorot","year":"2010"},{"key":"2023051607132057700_btab528-B6","volume-title":"Deep Learning","author":"Goodfellow","year":"2016"},{"key":"2023051607132057700_btab528-B7","year":"2020"},{"key":"2023051607132057700_btab528-B8","first-page":"369","author":"Graves","year":"2006"},{"key":"2023051607132057700_btab528-B9","author":"Gupta","year":"2020"},{"key":"2023051607132057700_btab528-B10","first-page":"14588","author":"Haase","year":"2020"},{"key":"2023051607132057700_btab528-B11","author":"Hinton","year":"2015"},{"key":"2023051607132057700_btab528-B12","first-page":"448","author":"Ioffe","year":"2015"},{"key":"2023051607132057700_btab528-B13","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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