{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:09Z","timestamp":1772138049257,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,17]],"date-time":"2021-09-17T00:00:00Z","timestamp":1631836800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"AMED P-CREATE","award":["JP20cm0106551"],"award-info":[{"award-number":["JP20cm0106551"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Here, we present Viola, a Python package that provides structural variant (SV; large scale genome DNA variations that can result in disease, e.g. cancer) signature analytical functions and utilities for custom SV classification, merging multi-SV-caller output files and SV annotation. We demonstrate that Viola can extract biologically meaningful SV signatures from publicly available SV data for cancer and we evaluate the computational time necessary for annotation of the data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Viola is available on pip (https:\/\/pypi.org\/project\/Viola-SV\/) and the source code is on GitHub (https:\/\/github.com\/dermasugita\/Viola-SV).<\/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\/btab662","type":"journal-article","created":{"date-parts":[[2021,9,14]],"date-time":"2021-09-14T07:19:56Z","timestamp":1631603996000},"page":"540-542","source":"Crossref","is-referenced-by-count":6,"title":["Viola: a structural variant signature extractor with user-defined classifications"],"prefix":"10.1093","volume":"38","author":[{"given":"Itsuki","family":"Sugita","sequence":"first","affiliation":[{"name":"Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo , Bunkyo-ku, Tokyo 1130033, Japan"},{"name":"Faculty of Medicine, Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 1138510, Japan"}]},{"given":"Shohei","family":"Matsuyama","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 1138510, Japan"}]},{"given":"Hiroki","family":"Dobashi","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Tokyo Medical and Dental University , Bunkyo-ku, Tokyo 1138510, Japan"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0038-728X","authenticated-orcid":false,"given":"Daisuke","family":"Komura","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo , Bunkyo-ku, Tokyo 1130033, Japan"}]},{"given":"Shumpei","family":"Ishikawa","sequence":"additional","affiliation":[{"name":"Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo , Bunkyo-ku, Tokyo 1130033, Japan"}]}],"member":"286","published-online":{"date-parts":[[2021,9,17]]},"reference":[{"key":"2023020108445720100_btab662-B2","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1101\/gr.222109.117","article-title":"GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly","volume":"27","author":"Cameron","year":"2017","journal-title":"Genome Res"},{"key":"2023020108445720100_btab662-B3","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.1038\/s41467-019-11146-4","article-title":"Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software","volume":"10","author":"Cameron","year":"2019","journal-title":"Nat. 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