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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]

PMID: 20639544

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