{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:33Z","timestamp":1753875873872,"version":"3.41.2"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,3,1]],"date-time":"2023-03-01T00:00:00Z","timestamp":1677628800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"name":"IPCC"},{"name":"Program at Freie Universit\u00e4t Berlin"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,19]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Alignment is the cornerstone of many long-read pipelines and plays an essential role in resolving structural variants (SVs). However, forced alignments of SVs embedded in long reads, inflexibility of integrating novel SVs models and computational inefficiency remain problems. Here, we investigate the feasibility of resolving long-read SVs with alignment-free algorithms. We ask: (1) Is it possible to resolve long-read SVs with alignment-free approaches? and (2) Does it provide an advantage over existing approaches? To this end, we implemented the framework named Linear, which can flexibly integrate alignment-free algorithms such as the generative model for long-read SV detection. Furthermore, Linear addresses the problem of compatibility of alignment-free approaches with existing software. It takes as input long reads and outputs standardized results existing software can directly process. We conducted large-scale assessments in this work and the results show that the sensitivity, and flexibility of Linear outperform alignment-based pipelines. Moreover, the computational efficiency is orders of magnitude faster.<\/jats:p>","DOI":"10.1093\/bib\/bbad071","type":"journal-article","created":{"date-parts":[[2023,3,4]],"date-time":"2023-03-04T12:54:49Z","timestamp":1677934489000},"source":"Crossref","is-referenced-by-count":0,"title":["Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models"],"prefix":"10.1093","volume":"24","author":[{"given":"Chenxu","family":"Pan","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin , Takustr. 9, Berlin 14195 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ren\u00e9","family":"Rahn","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin , Takustr. 9, Berlin 14195 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Heller","sequence":"additional","affiliation":[{"name":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics , Berlin 14195 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, Freie Universit\u00e4t Berlin , Takustr. 9, Berlin 14195 , Germany"},{"name":"Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics , Berlin 14195 , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,3,3]]},"reference":[{"issue":"6574","key":"2023032004555791000_","doi-asserted-by":"crossref","first-page":"abg8871","DOI":"10.1126\/science.abg8871","article-title":"Pangenomics enables genotyping of known structural variants in 5202 diverse 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