Monday, July 19, 2010

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

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/


Contact: svdetect@curie.fr


Supplementary information: Supplementary data are available at Bioinformatics online.


(this Post content was reproduced from: http://bioinformatics.oxfordjournals.org/cgi/content/short/26/15/1895?rss=1, Via Bioinformatics - current issue.)