{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,3]],"date-time":"2026-01-03T15:05:40Z","timestamp":1767452740045},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1004,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates.<\/jats:p>\n               <jats:p>Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools.<\/jats:p>\n               <jats:p>Availability and implementation: Socrates is released as open source and available from http:\/\/bioinf.wehi.edu.au\/socrates.<\/jats:p>\n               <jats:p>Contact: \u00a0papenfuss@wehi.edu.au<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt767","type":"journal-article","created":{"date-parts":[[2014,1,4]],"date-time":"2014-01-04T02:03:14Z","timestamp":1388800994000},"page":"1064-1072","source":"Crossref","is-referenced-by-count":69,"title":["Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads"],"prefix":"10.1093","volume":"30","author":[{"given":"Jan","family":"Schr\u00f6der","sequence":"first","affiliation":[{"name":"1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, 2Department of Medical Biology, University of Melbourne, Victoria 3010, 3Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 4Department of Pathology, The University of Melbourne, Victoria 3010, 5NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, 6Department of Computing and Information Systems, University of Melbourne, Victoria 3010, 7Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 8Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, 9Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and 10Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia"},{"name":"1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, 2Department of Medical Biology, University of Melbourne, Victoria 3010, 3Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 4Department of Pathology, The University of Melbourne, Victoria 3010, 5NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, 6Department of Computing and Information Systems, University of Melbourne, Victoria 3010, 7Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 8Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, 9Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and 10Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arthur","family":"Hsu","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Division, The Walter and Eliza 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Parkville, Victoria 3052, 2Department of Medical Biology, University of Melbourne, Victoria 3010, 3Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 4Department of Pathology, The University of Melbourne, Victoria 3010, 5NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, 6Department of Computing and Information Systems, University of Melbourne, Victoria 3010, 7Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 8Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, 9Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and 10Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia"},{"name":"1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, 2Department of Medical Biology, University of Melbourne, Victoria 3010, 3Melanoma Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 4Department of Pathology, The University of Melbourne, Victoria 3010, 5NICTA Victoria Laboratory, The University of Melbourne, Victoria 3010, 6Department of Computing and Information Systems, University of Melbourne, Victoria 3010, 7Cancer Therapeutics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, 8Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, 9Department of Mathematics and Statistics, The University of Melbourne, Victoria 3010 and 10Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoff","family":"Macintyre","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, 2Department of 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