{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T23:32:58Z","timestamp":1774999978380,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,5,30]],"date-time":"2023-05-30T00:00:00Z","timestamp":1685404800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Australian Medical Research Futures Fund","award":["MRF1173594"],"award-info":[{"award-number":["MRF1173594"]}]},{"name":"Australian Medical Research Futures Fund","award":["MRF2016008"],"award-info":[{"award-number":["MRF2016008"]}]},{"name":"Australian Research Council DECRA Fellowship","award":["DE230100178"],"award-info":[{"award-number":["DE230100178"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as \u2018basecalling\u2019, is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format \u2018SLOW5\u2019 to streamline and accelerate nanopore basecalling on high-performance computing (HPC) and cloud environments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>SLOW5 permits highly efficient sequential data access, eliminating a potential analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopore\u2019s Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Buttery-eel is available at https:\/\/github.com\/Psy-Fer\/buttery-eel.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad352","type":"journal-article","created":{"date-parts":[[2023,5,30]],"date-time":"2023-05-30T12:14:59Z","timestamp":1685448899000},"source":"Crossref","is-referenced-by-count":40,"title":["Accelerated nanopore basecalling with SLOW5 data format"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5812-1046","authenticated-orcid":false,"given":"Hiruna","family":"Samarakoon","sequence":"first","affiliation":[{"name":"Genomics Pillar, Garvan Institute of Medical Research , Sydney, NSW 2010, Australia"},{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children\u2019s Research Institute , Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW 2052, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6192-6937","authenticated-orcid":false,"given":"James M","family":"Ferguson","sequence":"additional","affiliation":[{"name":"Genomics Pillar, Garvan Institute of Medical Research , Sydney, NSW 2010, Australia"},{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children\u2019s Research Institute , Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9034-9905","authenticated-orcid":false,"given":"Hasindu","family":"Gamaarachchi","sequence":"additional","affiliation":[{"name":"Genomics Pillar, Garvan Institute of Medical Research , Sydney, NSW 2010, Australia"},{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children\u2019s Research Institute , Australia"},{"name":"School of Computer Science and Engineering, University of New South Wales , Sydney, NSW 2052, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3861-0472","authenticated-orcid":false,"given":"Ira W","family":"Deveson","sequence":"additional","affiliation":[{"name":"Genomics Pillar, Garvan Institute of Medical Research , Sydney, NSW 2010, Australia"},{"name":"Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children\u2019s Research Institute , Australia"},{"name":"Faculty of Medicine, University of New South Wales , Sydney, NSW 2052, 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