{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T17:40:10Z","timestamp":1727545210505},"reference-count":40,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T00:00:00Z","timestamp":1727481600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T00:00:00Z","timestamp":1727481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"DOI":"10.1186\/s12859-024-05937-w","type":"journal-article","created":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T17:01:51Z","timestamp":1727542911000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["FindCSV: a long-read based method for detecting complex structural variations"],"prefix":"10.1186","volume":"25","author":[{"given":"Yan","family":"Zheng","sequence":"first","affiliation":[]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,9,28]]},"reference":[{"issue":"7571","key":"5937_CR1","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nature15394","volume":"526","author":"PH Sudmant","year":"2015","unstructured":"Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 2015;526(7571):75\u201381.","journal-title":"Nature"},{"issue":"5","key":"5937_CR2","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/nrg2958","volume":"12","author":"C Alkan","year":"2011","unstructured":"Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363\u201376.","journal-title":"Nat Rev Genet"},{"issue":"9","key":"5937_CR3","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.tig.2016.07.002","volume":"32","author":"G Macintyre","year":"2016","unstructured":"Macintyre G, Ylstra B, Brenton JD. Sequencing structural variants in cancer for precision therapeutics. Trends Genet. 2016;32(9):530\u201342.","journal-title":"Trends Genet"},{"issue":"2","key":"5937_CR4","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/nrg3373","volume":"14","author":"J Weischenfeldt","year":"2013","unstructured":"Weischenfeldt J, Symmons O, Spitz F, Korbel JO. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet. 2013;14(2):125\u201338.","journal-title":"Nat Rev Genet"},{"issue":"1","key":"5937_CR5","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1038\/ng1718","volume":"38","author":"A Rovelet-Lecrux","year":"2006","unstructured":"Rovelet-Lecrux A, Hannequin D, Raux G, Meur NL, Laquerri\u00e8re A, Vital A, Dumanchin C, Feuillette S, Brice A, Vercelletto M, et al. App locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy. Nat Genet. 2006;38(1):24\u20136.","journal-title":"Nat Genet"},{"key":"5937_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/2040-2392-3-2","volume":"3","author":"DJ Hedges","year":"2012","unstructured":"Hedges DJ, Hamilton-Nelson KL, Sacharow SJ, Nations L, Beecham GW, Kozhekbaeva ZM, Butler BL, Cukier HN, Whitehead PL, Ma D, et al. Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci. Mol Autism. 2012;3:1\u201311.","journal-title":"Mol Autism"},{"issue":"18","key":"5937_CR7","doi-asserted-by":"publisher","first-page":"4712","DOI":"10.1111\/mec.14134","volume":"26","author":"S Dennenmoser","year":"2017","unstructured":"Dennenmoser S, Sedlazeck FJ, Iwaszkiewicz E, Li X-Y, Altm\u00fcller J, Nolte AW. Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin. Mol Ecol. 2017;26(18):4712\u201324.","journal-title":"Mol Ecol"},{"issue":"5","key":"5937_CR8","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1002\/em.21943","volume":"56","author":"JR Lupski","year":"2015","unstructured":"Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. Environ Mol Mutagen. 2015;56(5):419\u201336.","journal-title":"Environ Mol Mutagen"},{"issue":"5","key":"5937_CR9","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/ng.3834","volume":"49","author":"C Chiang","year":"2017","unstructured":"Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, et al. The impact of structural variation on human gene expression. Nat Genet. 2017;49(5):692\u20139.","journal-title":"Nat Genet"},{"issue":"3","key":"5937_CR10","doi-asserted-by":"publisher","first-page":"568","DOI":"10.1101\/gr.142646.112","volume":"23","author":"T Zichner","year":"2013","unstructured":"Zichner T, Garfield DA, Rausch T, St\u00fctz AM, Cannav\u00f3 E, Braun M, Furlong EE, Korbel JO. Impact of genomic structural variation in drosophila melanogaster based on population-scale sequencing. Genome Res. 2013;23(3):568\u201379.","journal-title":"Genome Res"},{"issue":"1","key":"5937_CR11","doi-asserted-by":"publisher","first-page":"14061","DOI":"10.1038\/ncomms14061","volume":"8","author":"DC Jeffares","year":"2017","unstructured":"Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, B\u00e4hler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun. 2017;8(1):14061.","journal-title":"Nat Commun"},{"issue":"1","key":"5937_CR12","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.tig.2011.10.002","volume":"28","author":"AR Quinlan","year":"2012","unstructured":"Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet. 2012;28(1):43\u201353.","journal-title":"Trends Genet"},{"issue":"10","key":"5937_CR13","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1016\/j.tig.2015.05.010","volume":"31","author":"B Weckselblatt","year":"2015","unstructured":"Weckselblatt B, Rudd MK. Human structural variation: mechanisms of chromosome rearrangements. Trends Genet. 2015;31(10):587\u201399.","journal-title":"Trends Genet"},{"issue":"1","key":"5937_CR14","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.cell.2020.08.006","volume":"183","author":"K Hadi","year":"2020","unstructured":"Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, et al. Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell. 2020;183(1):197\u2013210.","journal-title":"Cell"},{"issue":"18","key":"5937_CR15","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1093\/bioinformatics\/bts378","volume":"28","author":"T Rausch","year":"2012","unstructured":"Rausch T, Zichner T, Schlattl A, St\u00fctz AM, Benes V, Korbel JO. Delly: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28(18):333\u20139.","journal-title":"Bioinformatics"},{"key":"5937_CR16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2014-15-6-r84","volume":"15","author":"RM Layer","year":"2014","unstructured":"Layer RM, Chiang C, Quinlan AR, Hall IM. Lumpy: a probabilistic framework for structural variant discovery. Genome Biol. 2014;15:1\u201319.","journal-title":"Genome Biol"},{"issue":"8","key":"5937_CR17","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","volume":"32","author":"X Chen","year":"2016","unstructured":"Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, K\u00e4llberg M, Cox AJ, Kruglyak S, Saunders CT. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220\u20132.","journal-title":"Bioinformatics"},{"issue":"24","key":"5937_CR18","doi-asserted-by":"publisher","first-page":"3484","DOI":"10.1093\/bioinformatics\/btu431","volume":"30","author":"K Trappe","year":"2014","unstructured":"Trappe K, Emde A-K, Ehrlich H-C, Reinert K. Gustaf: detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics. 2014;30(24):3484\u201390.","journal-title":"Bioinformatics"},{"issue":"11","key":"5937_CR19","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1093\/bioinformatics\/btz261","volume":"37","author":"R Rajaby","year":"2021","unstructured":"Rajaby R, Sung W-K. Survindel: improving CNV calling from high-throughput sequencing data through statistical testing. Bioinformatics. 2021;37(11):1497\u2013505.","journal-title":"Bioinformatics"},{"key":"5937_CR20","doi-asserted-by":"crossref","unstructured":"Chen Y, Wang A, Barkley C, Zhao X, Gao M, Edmonds M, Chong Z. Debreak: deciphering the exact breakpoints of structural variations using long sequencing reads (2022)","DOI":"10.21203\/rs.3.rs-1261915\/v1"},{"key":"5937_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-020-02107-y","volume":"21","author":"T Jiang","year":"2020","unstructured":"Jiang T, Liu Y, Jiang Y, Li J, Gao Y, Cui Z, Liu Y, Liu B, Wang Y. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol. 2020;21:1\u201324.","journal-title":"Genome Biol"},{"issue":"6","key":"5937_CR22","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/s41592-018-0001-7","volume":"15","author":"FJ Sedlazeck","year":"2018","unstructured":"Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, Von Haeseler A, Schatz MC. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods. 2018;15(6):461\u20138.","journal-title":"Nat Methods"},{"key":"5937_CR23","doi-asserted-by":"crossref","unstructured":"Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, et al. Comprehensive structural variant detection: from mosaic to population-level. BioRxiv. 2022-04 (2022)","DOI":"10.1101\/2022.04.04.487055"},{"issue":"1","key":"5937_CR24","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.1038\/s41467-017-01343-4","volume":"8","author":"M Cretu Stancu","year":"2017","unstructured":"Cretu Stancu M, Van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, De Ligt J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, et al. Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nat Commun. 2017;8(1):1326.","journal-title":"Nat Commun"},{"issue":"6","key":"5937_CR25","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1038\/s41592-018-0002-6","volume":"15","author":"L Gong","year":"2018","unstructured":"Gong L, Wong C-H, Cheng W-C, Tjong H, Menghi F, Ngan CY, Liu ET, Wei C-L. Picky comprehensively detects high-resolution structural variants in nanopore long reads. Nat Methods. 2018;15(6):455\u201360.","journal-title":"Nat Methods"},{"issue":"17","key":"5937_CR26","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1093\/bioinformatics\/btz041","volume":"35","author":"D Heller","year":"2019","unstructured":"Heller D, Vingron M. SVIM: structural variant identification using mapped long reads. Bioinformatics. 2019;35(17):2907\u201315.","journal-title":"Bioinformatics"},{"key":"5937_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-15-180","volume":"15","author":"AC English","year":"2014","unstructured":"English AC, Salerno WJ, Reid JG. Pbhoney: identifying genomic variants via long-read discordance and interrupted mapping. BMC Bioinform. 2014;15:1\u20137.","journal-title":"BMC Bioinform"},{"issue":"10","key":"5937_CR28","doi-asserted-by":"publisher","first-page":"1230","DOI":"10.1038\/s41592-022-01609-w","volume":"19","author":"J Lin","year":"2022","unstructured":"Lin J, Wang S, Audano PA, Meng D, Flores JI, Kosters W, Yang X, Jia P, Marschall T, Beck CR, et al. SVision: a deep learning approach to resolve complex structural variants. Nat Methods. 2022;19(10):1230\u20133.","journal-title":"Nat Methods"},{"key":"5937_CR29","doi-asserted-by":"crossref","unstructured":"Zheng Y, Shang X. SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data. BMC Bioinform. 2023;24.","DOI":"10.1186\/s12859-023-05324-x"},{"issue":"3","key":"5937_CR30","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/s41576-019-0180-9","volume":"21","author":"SS Ho","year":"2020","unstructured":"Ho SS, Urban AE, Mills RE. Structural variation in the sequencing era. Nat Rev Genet. 2020;21(3):171\u201389.","journal-title":"Nat Rev Genet"},{"key":"5937_CR31","doi-asserted-by":"publisher","first-page":"432668","DOI":"10.3389\/fgene.2019.00426","volume":"10","author":"T Mantere","year":"2019","unstructured":"Mantere T, Kersten S, Hoischen A. Long-read sequencing emerging in medical genetics. Front Genet. 2019;10:432668.","journal-title":"Front Genet"},{"key":"5937_CR32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-018-1505-2","volume":"19","author":"H Dashnow","year":"2018","unstructured":"Dashnow H, Lek M, Phipson B, Halman A, Sadedin S, Lonsdale A, Davis M, Lamont P, Clayton JS, Laing NG, et al. Stretch: detecting and discovering pathogenic short tandem repeat expansions. Genome Biol. 2018;19:1\u201313.","journal-title":"Genome Biol"},{"issue":"1","key":"5937_CR33","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1186\/s13059-021-02447-3","volume":"22","author":"R Chiu","year":"2021","unstructured":"Chiu R, Rajan-Babu I-S, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol. 2021;22(1):224.","journal-title":"Genome Biol"},{"key":"5937_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2013-14-6-405","volume":"14","author":"RJ Roberts","year":"2013","unstructured":"Roberts RJ, Carneiro MO, Schatz MC. The advantages of SMRT sequencing. Genome Biol. 2013;14:1\u20134.","journal-title":"Genome Biol"},{"key":"5937_CR35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-015-0866-z","volume":"17","author":"M Jain","year":"2016","unstructured":"Jain M, Olsen HE, Paten B, Akeson M. The oxford nanopore minion: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016;17:1\u201311.","journal-title":"Genome Biol"},{"issue":"11","key":"5937_CR36","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1038\/s41587-020-0538-8","volume":"38","author":"JM Zook","year":"2020","unstructured":"Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, et al. A robust benchmark for detection of germline large deletions and insertions. Nat Biotechnol. 2020;38(11):1347\u201355.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"5937_CR37","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/s41597-020-00743-4","volume":"7","author":"T Hon","year":"2020","unstructured":"Hon T, Mars K, Young G, Tsai Y-C, Karalius JW, Landolin JM, Maurer N, Kudrna D, Hardigan MA, Steiner CC, et al. Highly accurate long-read HiFi sequencing data for five complex genomes. Sci Data. 2020;7(1):399.","journal-title":"Sci Data"},{"issue":"3","key":"5937_CR38","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1038\/s41587-020-0711-0","volume":"39","author":"S Garg","year":"2021","unstructured":"Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, et al. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol. 2021;39(3):309\u201312.","journal-title":"Nat Biotechnol"},{"issue":"6588","key":"5937_CR39","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","volume":"376","author":"S Nurk","year":"2022","unstructured":"Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, et al. The complete sequence of a human genome. Science. 2022;376(6588):44\u201353.","journal-title":"Science"},{"key":"5937_CR40","doi-asserted-by":"crossref","unstructured":"1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491(7422):56.","DOI":"10.1038\/nature11632"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05937-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-024-05937-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-024-05937-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T17:02:37Z","timestamp":1727542957000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-024-05937-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,28]]},"references-count":40,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["5937"],"URL":"https:\/\/doi.org\/10.1186\/s12859-024-05937-w","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,28]]},"assertion":[{"value":"24 March 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 September 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not Applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval consent to participate"}},{"value":"Not Applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"315"}}