{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,3]],"date-time":"2026-01-03T15:20:04Z","timestamp":1767453604059},"reference-count":21,"publisher":"Springer Science and Business Media LLC","issue":"S14","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Structural variations (SVs) change the structure of the genome and are therefore the causes of various diseases. Next-generation sequencing allows us to obtain a multitude of sequence data, some of which can be used to infer the position of SVs.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Methods<\/jats:title>\n            <jats:p>We developed a new method and implementation named ClipCrop for detecting SVs with single-base resolution using soft-clipping information. A soft-clipped sequence is an unmatched fragment in a partially mapped read. To assess the performance of ClipCrop with other SV-detecting tools, we generated various patterns of simulation data \u2013 SV lengths, read lengths, and the depth of coverage of short reads \u2013 with insertions, deletions, tandem duplications, inversions and single nucleotide alterations in a human chromosome. For comparison, we selected BreakDancer, CNVnator and Pindel, each of which adopts a different approach to detect SVs, e.g. discordant pair approach, depth of coverage approach and split read approach, respectively.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Our method outperformed BreakDancer and CNVnator in both discovering rate and call accuracy in any type of SV. Pindel offered a similar performance as our method, but our method crucially outperformed for detecting small duplications. From our experiments, ClipCrop infer reliable SVs for the data set with more than 50 bases read lengths and 20x depth of coverage, both of which are reasonable values in current NGS data set.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>ClipCrop can detect SVs with higher discovering rate and call accuracy than any other tool in our simulation data set.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-s14-s7","type":"journal-article","created":{"date-parts":[[2011,12,14]],"date-time":"2011-12-14T19:38:32Z","timestamp":1323891512000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information"],"prefix":"10.1186","volume":"12","author":[{"given":"Shin","family":"Suzuki","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomohiro","family":"Yasuda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuichi","family":"Shiraishi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satoru","family":"Miyano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,12,14]]},"reference":[{"issue":"11","key":"4966_CR1","doi-asserted-by":"publisher","first-page":"S13","DOI":"10.1038\/nmeth.1374","volume":"6","author":"Paul Medvedev","year":"2009","unstructured":"Medvedev Paul, Stanciu Monica, Brudno Michael: Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods 2009, 6(11):S13-S20. 10.1038\/nmeth.1374","journal-title":"Nat. Methods"},{"key":"4966_CR2","doi-asserted-by":"publisher","first-page":"S37","DOI":"10.1038\/ng2080","volume":"39","author":"Steven A McCarroll","year":"2009","unstructured":"McCarroll StevenA, Altshuler DavidM: Copy-number variation and association studies of human disease. Nat. Genetics 2009, 39: S37-S42.","journal-title":"Nat. Genetics"},{"key":"4966_CR3","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1126\/science.1138659","volume":"316","author":"J Sebat","year":"2007","unstructured":"Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtim\u00e4ki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M: Strong association of de novo copy number mutations with autism. Science 2007, 316: 445\u2013449. 10.1126\/science.1138659","journal-title":"Science"},{"key":"4966_CR4","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1126\/science.1090278","volume":"302","author":"AB Singleton","year":"2003","unstructured":"Singleton AB, Farrer M, Johnson J, Singleton A, Hague S, Kachergus J, Hulihan M, Peuralinna T, Dutra A, Nussbaum R, Lincoln S, Crawley A, Hanson M, Maraganore D, Adler C, Cookson MR, Muenter M, Baptista M, Miller D, Blancato J, Hardy J, Gwinn-Hardy K: Alpha-synuclein locus triplication causes Parkinson\u2019s disease. Science 2003, 302: 841. 10.1126\/science.1090278","journal-title":"Science"},{"key":"4966_CR5","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1038\/ng.162","volume":"40","author":"B Xu","year":"2008","unstructured":"Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M: Strong association of de novo copy number mutations with sporadic schizophrenia. Nat. Genetics 2008, 40: 880\u2013885. 10.1038\/ng.162","journal-title":"Nat. Genetics"},{"key":"4966_CR6","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/gm62","volume":"1","author":"Adam Shlien","year":"2009","unstructured":"Shlien Adam, Malkin David: Copy number variations and cancer. Genome Medicine 2009, 1: 62. 10.1186\/gm62","journal-title":"Genome Medicine"},{"key":"4966_CR7","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1038\/nrg2795","volume":"11","author":"RDavid Hawkins","year":"2010","unstructured":"Hawkins R, Hon GaryC., Ren Bing: Next-generation genomics : an integrative approach. Nature Reviews Genetics 2010, 11: 476\u2013486.","journal-title":"Nature Reviews Genetics"},{"key":"4966_CR8","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1126\/science.1149504","volume":"318","author":"JO Korbel","year":"2007","unstructured":"Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M: Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318: 420\u2013426. 10.1126\/science.1149504","journal-title":"Science"},{"key":"4966_CR9","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1038\/nmeth.1363","volume":"6","author":"K Chen","year":"2009","unstructured":"Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER: BreakDancer: An algorithm for high resolution mapping of genomic structural variation. Nat. Methods 2009, 6: 677\u2013681. 10.1038\/nmeth.1363","journal-title":"Nat. Methods"},{"key":"4966_CR10","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1101\/gr.088633.108","volume":"19","author":"F Hormozdiari","year":"2009","unstructured":"Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC: Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 2009, 19: 1527\u20131541. 10.1101\/gr.091868.109","journal-title":"Genome Res"},{"key":"4966_CR11","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1038\/nmeth.f.256","volume":"6","author":"S Lee","year":"2009","unstructured":"Lee S, et al.: MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods 2009, 6: 473\u2013474. 10.1038\/nmeth.f.256","journal-title":"Nat. Methods"},{"key":"4966_CR12","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1101\/gr.088633.108","volume":"19","author":"F Hormozdiari","year":"2009","unstructured":"Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC: Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009, 19: 1527\u20131541. 10.1101\/gr.091868.109","journal-title":"Genome Res"},{"key":"4966_CR13","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1038\/nmeth.1276","volume":"6","author":"DY Chiang","year":"2009","unstructured":"Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 2009, 6: 99\u2013103. 10.1038\/nmeth.1276","journal-title":"Nat. Methods"},{"key":"4966_CR14","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov A, Urban AE, Snyder M, Gerstein M: CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011, 21: 974\u2013984. 10.1101\/gr.114876.110","journal-title":"Genome Res"},{"issue":"21","key":"4966_CR15","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","volume":"25","author":"K Ye","year":"2009","unstructured":"Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect breakpoints of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25(21):2865\u20132871. 10.1093\/bioinformatics\/btp394","journal-title":"Bioinformatics"},{"issue":"21","key":"4966_CR16","doi-asserted-by":"publisher","first-page":"2684","DOI":"10.1093\/bioinformatics\/btq528","volume":"26","author":"HJ Abel","year":"2010","unstructured":"Abel HJ, Duncavage EJ, Becker N, Armstrong JR, Magrini VJ, Pfeifer JD: SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics 2010, 26(21):2684\u20132688. 10.1093\/bioinformatics\/btq528","journal-title":"Bioinformatics"},{"issue":"14","key":"4966_CR17","doi-asserted-by":"publisher","first-page":"2684","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"Heng Li","year":"2009","unstructured":"Li Heng, Durbin Richard: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):2684\u20132688.","journal-title":"Bioinformatics"},{"issue":"16","key":"4966_CR18","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup: The sequence alignment\/map format and SAMtools. Bioinformatics 2009, 25(16):2078\u20132079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"key":"4966_CR19","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J. Mol. Biol 1990, 215: 403\u2013410.","journal-title":"J. Mol. Biol"},{"key":"4966_CR20","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1101\/gr.229202. Article published online before March 2002","volume":"12","author":"WJames Kent","year":"2002","unstructured":"Kent W: BLAT \u2013 The BLAST-Like Alignment Tool. Genome Res 2002, 12: 656\u2013664.","journal-title":"Genome Res"},{"issue":"8","key":"4966_CR21","doi-asserted-by":"publisher","first-page":"652","DOI":"10.1038\/nmeth.1628","volume":"8","author":"J Wang","year":"2011","unstructured":"Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J: CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods 2011, 8(8):652\u2013654. 10.1038\/nmeth.1628","journal-title":"Nat. Methods"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S14-S7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T17:50:00Z","timestamp":1630518600000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S14-S7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12]]},"references-count":21,"journal-issue":{"issue":"S14","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4966"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s14-s7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,12]]},"assertion":[{"value":"14 December 2011","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S7"}}