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

Bioinformatics
Bruno ZeitouniEmmanuel Barillot

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. Source code and sample data are available at http://svdetect.sourceforge.net/

References

Mar 3, 2004·Nature Reviews. Cancer·P Andrew FutrealMichael R Stratton
May 30, 2009·Bioinformatics·Suzanne SindiBenjamin J Raphael
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra

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Citations

Jul 10, 2012·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Binnaz YalcinThomas M Keane
Oct 19, 2013·Nature Communications·Shengxiong HuangYongsheng Liu
Feb 26, 2011·Human Molecular Genetics·Wigard P KloostermanEdwin Cuppen
Feb 15, 2013·Biological Procedures Online·Derek Shyr, Qi Liu
Sep 11, 2012·Journal of Animal Science and Biotechnology·Yongsheng BaiJames Cavalcoli
May 17, 2014·PLoS Genetics·Michaela DrögemüllerTosso Leeb
Oct 3, 2012·PloS One·Andrew TrittAaron E Darling
Jul 8, 2014·Oncogenesis·R BelaniA Torkamani
Feb 3, 2016·Nature Communications·Chloé LescaleLudovic Deriano
Dec 23, 2015·Molecular Therapy : the Journal of the American Society of Gene Therapy·Jaichandran SivalingamOi Lian Kon
Mar 3, 2015·Proceedings of the National Academy of Sciences of the United States of America·Christof OsmanPeter Walter
May 16, 2013·International Journal of Food Microbiology·Guozhong ZhaoXiaohong Cao
Jun 25, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ji QiHong Ma
Sep 4, 2013·Journal of Cellular and Molecular Medicine·Xiaoming ZhuJun Cai
Dec 24, 2010·Annals of the New York Academy of Sciences·Alexandra I F Blakemore, Philippe Froguel
Jun 15, 2013·Genes, Chromosomes & Cancer·Brian A WalkerGareth J Morgan
Oct 10, 2015·Database : the Journal of Biological Databases and Curation·Manonanthini Thangam, Ramesh Kumar Gopal

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Software Mentioned

SVDetect
GASV
Circos

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