SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Bruno Zeitouni; Valentina Boeva; Isabelle Janoueix-Lerosey; Sophie Loeillet; Patricia Legoix-Né; Alain Nicolas; Olivier Delattre; Emmanuel Barillot

doi:10.1093/bioinformatics/btq293

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

Bruno Zeitouni ^{1, *} Valentina Boeva ¹ Isabelle Janoueix-Lerosey ² Sophie Loeillet ³ Patricia Legoix-Né ⁴ Alain Nicolas ³ Olivier Delattre ² Emmanuel Barillot ^{1, *}

* Corresponding author

1 Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe

2 U830 - Unité de génétique et biologie des cancers

3 DIG CANCER - Dynamique de l'information génétique : bases fondamentales et cancer

4 Institut Curie

Abstract : We present SVDetect, a program designed to identify genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them according to their type, e.g. large insertions–deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations. SVDetect outputs predicted structural variants in various file formats for appropriate graphical visualization. Availability: Source code and sample data are available at http://svdetect.sourceforge.net/

Keywords : cancer genome structural variations paired-end sequencing tool

Document type :

Journal articles

Domain :

Life Sciences [q-bio] / Quantitative Methods [q-bio.QM]

Computer Science [cs] / Bioinformatics [q-bio.QM]

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https://www.hal.inserm.fr/inserm-00508372
Contributor : Bruno Zeitouni <>
Submitted on : Tuesday, August 3, 2010 - 11:43:37 AM
Last modification on : Thursday, April 11, 2019 - 4:02:12 PM
Document(s) archivé(s) le : Thursday, November 4, 2010 - 10:39:34 AM

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

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SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

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