{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T02:48:10Z","timestamp":1776480490494,"version":"3.51.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2016,10,7]],"date-time":"2016-10-07T00:00:00Z","timestamp":1475798400000},"content-version":"vor","delay-in-days":2660,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: There is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. Indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging.<\/jats:p>\n               <jats:p>Results: We present Pindel, a pattern growth approach, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads. We use both simulated reads and real data to demonstrate the efficiency of the computer program and accuracy of the results.<\/jats:p>\n               <jats:p>Availability: The binary code and a short user manual can be freely downloaded from http:\/\/www.ebi.ac.uk\/\u223ckye\/pindel\/.<\/jats:p>\n               <jats:p>Contact: \u00a0k.ye@lumc.nl; zn1@sanger.ac.uk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp394","type":"journal-article","created":{"date-parts":[[2009,6,27]],"date-time":"2009-06-27T00:24:20Z","timestamp":1246062260000},"page":"2865-2871","source":"Crossref","is-referenced-by-count":1852,"title":["Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads"],"prefix":"10.1093","volume":"25","author":[{"given":"Kai","family":"Ye","sequence":"first","affiliation":[{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"},{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Marcel H.","family":"Schulz","sequence":"additional","affiliation":[{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"},{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Quan","family":"Long","sequence":"additional","affiliation":[{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Rolf","family":"Apweiler","sequence":"additional","affiliation":[{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]},{"given":"Zemin","family":"Ning","sequence":"additional","affiliation":[{"name":"1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK"}]}],"member":"286","published-online":{"date-parts":[[2009,6,26]]},"reference":[{"key":"2023013112193974000_B1","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1534\/genetics.104.031757","article-title":"Natural genetic 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