{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T17:10:33Z","timestamp":1767892233875,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,12,18]],"date-time":"2025-12-18T00:00:00Z","timestamp":1766016000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2022YFF1202101"],"award-info":[{"award-number":["2022YFF1202101"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2024YFC3406303"],"award-info":[{"award-number":["2024YFC3406303"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62472120"],"award-info":[{"award-number":["62472120"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62402140"],"award-info":[{"award-number":["62402140"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Nanopore sequencing technology enables real-time sequencing and is widely used in rapid detection applications. However, in clinical scenarios, existing structural variant (SV) detection tools typically separate sequencing from computation, limiting their timeliness for clinical applications. To address this, we introduce cuteSV-OL, a novel framework designed for real-time SV discovery, which can be embedded within nanopore sequencing instruments to analyze data concurrently with its generation. Additionally, cuteSV-OL features a real-time SV detection rate evaluation module, allowing users to terminate sequencing early when appropriate, thereby reducing time and cost. Experimental results show that on a standard desktop computer, cuteSV-OL can perform real-time analysis during sequencing and complete SV calling within min after sequencing ends, achieving performance comparable to offline methods. This approach has the potential to enhance rapid clinical diagnostics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>cuteSV-OL is released under the MIT license and is available at https:\/\/github.com\/gwmHIT\/cuteSV-OL. It can also be installed via Bioconda or accessed through https:\/\/doi.org\/10.5281\/zenodo.17777436.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf668","type":"journal-article","created":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T12:53:10Z","timestamp":1765630390000},"source":"Crossref","is-referenced-by-count":0,"title":["cuteSV-OL: a real-time structural variation detection framework for nanopore sequencing devices"],"prefix":"10.1093","volume":"42","author":[{"given":"Weimin","family":"Guo","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, Faculty of Computing, Harbin Institute of Technology , Harbin, Heilongjiang 150001,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8385-1908","authenticated-orcid":false,"given":"Yadong","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Faculty of Computing, Harbin Institute of Technology , Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , Zhengzhou, Henan 450000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6500-6217","authenticated-orcid":false,"given":"Yadong","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Faculty of Computing, Harbin Institute of Technology , Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , Zhengzhou, Henan 450000,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0673-8503","authenticated-orcid":false,"given":"Tao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Faculty of Computing, Harbin Institute of Technology , Harbin, Heilongjiang 150001,","place":["China"]},{"name":"Zhengzhou Research Institute, Harbin Institute of Technology , Zhengzhou, Henan 450000,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"2026010711363362400_btaf668-B1","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1038\/s41592-023-01932-w","article-title":"A survey of algorithms for the detection of genomic structural variants from long-read sequencing data","volume":"20","author":"Ahsan","year":"2023","journal-title":"Nat Methods"},{"key":"2026010711363362400_btaf668-B2","doi-asserted-by":"crossref","first-page":"eabf7117","DOI":"10.1126\/science.abf7117","article-title":"Haplotype-resolved diverse human genomes and integrated analysis of structural variation","volume":"372","author":"Ebert","year":"2021","journal-title":"Science"},{"key":"2026010711363362400_btaf668-B3","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1038\/s41587-022-01221-5","article-title":"Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing","volume":"40","author":"Goenka","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026010711363362400_btaf668-B4","unstructured":"Guo W. \u00a0cuteSV-OL-v1.0.2. 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