{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:18:41Z","timestamp":1760955521945},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation : Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent \u2018third-generation\u2019 sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates.<\/jats:p>\n               <jats:p>Results : We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.<\/jats:p>\n               <jats:p>Availability and implementation : MultiBreak-SV is available at http:\/\/compbio.cs.brown.edu\/software\/ .<\/jats:p>\n               <jats:p>Contact : annaritz@vt.edu or braphael@cs.brown.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu714","type":"journal-article","created":{"date-parts":[[2014,10,30]],"date-time":"2014-10-30T05:01:31Z","timestamp":1414645291000},"page":"3458-3466","source":"Crossref","is-referenced-by-count":53,"title":["Characterization of structural variants with single molecule and hybrid sequencing approaches"],"prefix":"10.1093","volume":"30","author":[{"given":"Anna","family":"Ritz","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Brown University, RI 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY 4 School of Natural Sciences, University of California, Merced, CA 5 Pacific Biosciences, Menlo Park, CA 6 Center for Computational Molecular Biology, Brown University, RI"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ali","family":"Bashir","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Brown University, RI 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY 4 School of Natural Sciences, University of California, Merced, CA 5 Pacific Biosciences, Menlo Park, CA 6 Center for Computational Molecular Biology, Brown University, RI"},{"name":"1 Department of Computer Science, Brown University, RI 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY 4 School of Natural Sciences, University of California, Merced, CA 5 Pacific Biosciences, Menlo Park, CA 6 Center for Computational Molecular Biology, Brown University, RI"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suzanne","family":"Sindi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Brown University, RI 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, NY 3 Institute for Genomics and Multiscale Biology, Icahn School of Medicine, Mount Sinai, NY 4 School of Natural Sciences, University of California, Merced, CA 5 Pacific Biosciences, Menlo Park, CA 6 Center for 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