{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,6]],"date-time":"2026-07-06T23:53:13Z","timestamp":1783381993868,"version":"3.54.6"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,7]],"date-time":"2019-10-07T00:00:00Z","timestamp":1570406400000},"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\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["773026"],"award-info":[{"award-number":["773026"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"AIRC Investigator","award":["20307"],"award-info":[{"award-number":["20307"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>VISOR is a tool for haplotype-specific simulations of simple and complex structural variants (SVs). The method is applicable to haploid, diploid or higher ploidy simulations for bulk or single-cell sequencing data. SVs are implanted into FASTA haplotypes at single-basepair resolution, optionally with nearby single-nucleotide variants. Short or long reads are drawn at random from these haplotypes using standard error profiles. Double- or single-stranded data can be simulated and VISOR supports the generation of haplotype-tagged BAM files. The tool further includes methods to interactively visualize simulated variants in single-stranded data. The versatility of VISOR is unmet by comparable tools and it lays the foundation to simulate haplotype-resolved cancer heterogeneity data in bulk or at single-cell resolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>VISOR is implemented in python 3.6, open-source and freely available at https:\/\/github.com\/davidebolo1993\/VISOR. Documentation is available at https:\/\/davidebolo1993.github.io\/visordoc\/.<\/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\/btz719","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T12:36:14Z","timestamp":1569933374000},"page":"1267-1269","source":"Crossref","is-referenced-by-count":52,"title":["VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8735-8093","authenticated-orcid":false,"given":"Davide","family":"Bolognini","sequence":"first","affiliation":[{"name":"Department of Experimental and Clinical Medicine, University of Florence , Florence 50134, Italy"},{"name":"European Molecular Biology Laboratory (EMBL) , GeneCore, Heidelberg 69917, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashley","family":"Sanders","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL) , Genome Biology Unit, Heidelberg 69917, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan O","family":"Korbel","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL) , Genome Biology Unit, Heidelberg 69917, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Magi","sequence":"additional","affiliation":[{"name":"Department of Information Engineering, University of Florence , Florence 50134, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vladimir","family":"Benes","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL) , GeneCore, Heidelberg 69917, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5773-5620","authenticated-orcid":false,"given":"Tobias","family":"Rausch","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory (EMBL) , GeneCore, Heidelberg 69917, Germany"},{"name":"European Molecular Biology Laboratory (EMBL) , Genome Biology Unit, Heidelberg 69917, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,10,7]]},"reference":[{"key":"2023013110132898700_btz719-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023013110132898700_btz719-B2","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nrg2958","article-title":"Genome structural variation discovery and genotyping","volume":"12","author":"Alkan","year":"2011","journal-title":"Nat. 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