{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:11:44Z","timestamp":1772172704354,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007737","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,3,27]],"date-time":"2020-03-27T00:00:00Z","timestamp":1585267200000}}],"reference-count":30,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T00:00:00Z","timestamp":1584403200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30CA044579"],"award-info":[{"award-number":["P30CA044579"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007737","type":"journal-article","created":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T13:42:38Z","timestamp":1584452558000},"page":"e1007737","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1898-8769","authenticated-orcid":true,"given":"Kunal","family":"Kathuria","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0782-3056","authenticated-orcid":true,"given":"Aakrosh","family":"Ratan","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,3,17]]},"reference":[{"key":"pcbi.1007737.ref001","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/nrg3373","article-title":"Phenotypic impact of genomic structural variation: insights from and for human disease","volume":"14","author":"J Weischenfeldt","year":"2013","journal-title":"Nature reviews Genetics"},{"key":"pcbi.1007737.ref002","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/ng1696","article-title":"Common deletion polymorphisms in the human genome","volume":"38","author":"SA McCarroll","year":"2006","journal-title":"Nature genetics"},{"key":"pcbi.1007737.ref003","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s13039-014-0086-3","article-title":"Deletions and duplications of the 22q11.2 region in spermatozoa from DiGeorge\/velocardiofacial fathers","volume":"7","author":"L Verg\u00e9s","year":"2014","journal-title":"Molecular cytogenetics"},{"issue":"5","key":"pcbi.1007737.ref004","first-page":"1184","article-title":"Molecular analysis of deletion (17)(p11. 2p11. 2) in a family segregating a 17p paracentric inversion: implications for carriers of paracentric inversions","volume":"60","author":"SP Yang","year":"1997","journal-title":"American journal of human genetics"},{"key":"pcbi.1007737.ref005","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":"DL Cameron","year":"2019","journal-title":"Nature communications"},{"key":"pcbi.1007737.ref006","doi-asserted-by":"crossref","first-page":"R84","DOI":"10.1186\/gb-2014-15-6-r84","article-title":"LUMPY: a probabilistic framework for structural variant discovery","volume":"15","author":"RM Layer","year":"2014","journal-title":"Genome biology"},{"key":"pcbi.1007737.ref007","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.11168.1","article-title":"TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data","volume":"6","author":"J Eisfeldt","year":"2017","journal-title":"F1000Research"},{"key":"pcbi.1007737.ref008","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2017.05.030","article-title":"Toolkit for automated and rapid discovery of structural variants","volume":"129","author":"A Soylev","year":"2017","journal-title":"Methods (San Diego, Calif)"},{"key":"pcbi.1007737.ref009","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ymeth.2016.01.020","article-title":"Structural variation detection using next-generation sequencing data: A comparative technical review","volume":"102","author":"P Guan","year":"2016","journal-title":"Methods (San Diego, Calif)"},{"key":"pcbi.1007737.ref010","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1093\/bib\/bbu047","article-title":"Making the difference: integrating structural variation detection tools","volume":"16","author":"K Lin","year":"2015","journal-title":"Briefings in bioinformatics"},{"key":"pcbi.1007737.ref011","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1093\/bfgp\/elv014","article-title":"A decade of structural variants: description, history and methods to detect structural variation","volume":"14","author":"G Escaram\u00eds","year":"2015","journal-title":"Briefings in functional genomics"},{"key":"pcbi.1007737.ref012","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1126\/science.1149504","article-title":"Paired-end mapping reveals extensive structural variation in the human genome","volume":"318","author":"JO Korbel","year":"2007","journal-title":"Science (New York, NY)"},{"key":"pcbi.1007737.ref013","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13100-015-0055-3","article-title":"Transposable element detection from whole genome sequence data","volume":"6","author":"AD Ewing","year":"2015","journal-title":"Mobile DNA"},{"key":"pcbi.1007737.ref014","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/0092-8674(93)90078-5","article-title":"Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition","volume":"72","author":"DD Luan","year":"1993","journal-title":"Cell"},{"key":"pcbi.1007737.ref015","doi-asserted-by":"crossref","first-page":"3923","DOI":"10.1093\/bioinformatics\/btz237","article-title":"Discovery of tandem and interspersed segmental duplications using high-throughput sequencing","volume":"35","author":"A Soylev","year":"2019","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref016","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"PH Sudmant","year":"2015","journal-title":"Nature"},{"key":"pcbi.1007737.ref017","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1093\/bioinformatics\/bts566","article-title":"CLEVER: clique-enumerating variant finder","volume":"28","author":"T Marschall","year":"2012","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref018","doi-asserted-by":"crossref","first-page":"i333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"T Rausch","year":"2012","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref019","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"X Chen","year":"2016","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref020","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","article-title":"SpeedSeq: ultra-fast personal genome analysis and interpretation","volume":"12","author":"C Chiang","year":"2015","journal-title":"Nature methods"},{"key":"pcbi.1007737.ref021","doi-asserted-by":"crossref","first-page":"1679","DOI":"10.1093\/bioinformatics\/btt198","article-title":"RSVSim: an R\/Bioconductor package for the simulation of structural variations","volume":"29","author":"C Bartenhagen","year":"2013","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref022","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013."},{"key":"pcbi.1007737.ref023","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"pcbi.1007737.ref024","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1186\/s12864-015-1479-3","article-title":"Assessing structural variation in a personal genome-towards a human reference diploid genome","volume":"16","author":"AC English","year":"2015","journal-title":"BMC genomics"},{"key":"pcbi.1007737.ref025","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/nature13907","article-title":"Resolving the complexity of the human genome using single-molecule sequencing","volume":"517","author":"MJP Chaisson","year":"2015","journal-title":"Nature"},{"key":"pcbi.1007737.ref026","doi-asserted-by":"crossref","first-page":"W194","DOI":"10.1093\/nar\/gky464","article-title":"LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis","volume":"46","author":"VP Nagraj","year":"2018","journal-title":"Nucleic acids research"},{"key":"pcbi.1007737.ref027","doi-asserted-by":"crossref","first-page":"e30377","DOI":"10.1371\/journal.pone.0030377","article-title":"Fast computation and applications of genome mappability","volume":"7","author":"T Derrien","year":"2012","journal-title":"PloS one"},{"key":"pcbi.1007737.ref028","doi-asserted-by":"crossref","first-page":"i350","DOI":"10.1093\/bioinformatics\/btq216","article-title":"Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery","volume":"26","author":"F Hormozdiari","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"pcbi.1007737.ref029","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.tcs.2006.06.015","article-title":"The worst-case time complexity for generating all maximal cliques and computational experiments","volume":"363","author":"E Tomita","year":"2006","journal-title":"Theoretical Computer Science"},{"key":"pcbi.1007737.ref030","unstructured":"Hagberg A, Swart P, S Chult D. Exploring network structure, dynamics, and function using NetworkX. Los Alamos National Lab.(LANL), Los Alamos, NM (United States); 2008."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007737","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,3,27]],"date-time":"2020-03-27T00:00:00Z","timestamp":1585267200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007737","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,3,27]],"date-time":"2020-03-27T13:36:09Z","timestamp":1585316169000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007737"}},"subtitle":[],"editor":[{"given":"Jian","family":"Ma","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,3,17]]},"references-count":30,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007737","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/469981","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,17]]}}}