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


ABSTRACT: SUMMARY: 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/

SUBMITTER: Zeitouni B 

PROVIDER: S-EPMC2905550 | biostudies-other | 2010 Aug

REPOSITORIES: biostudies-other

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

Zeitouni Bruno B   Boeva Valentina V   Janoueix-Lerosey Isabelle I   Loeillet Sophie S   Legoix-né Patricia P   Nicolas Alain A   Delattre Olivier O   Barillot Emmanuel E  

Bioinformatics (Oxford, England) 20100801 15


<h4>Summary</h4>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 un  ...[more]

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