SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data - PubMed (original) (raw)

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

Bruno Zeitouni et al. Bioinformatics. 2010.

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/

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Figures

Fig. 1.

Overview of SVDetect algorithm and output. (A) The workflow. (B) Graphical visualization of predicted SVs. Genomic locations of inter- and intra-chromosomal links are shown using the Circos software. Starting from outside of the circle, the following features are displayed: chromosome ideograms, scatter plot of the copy-number profile and color-coded spans of chromosomal links.

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