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


BACKGROUND
Source code and sample data are available at http://svdetect.sourceforge.net/
Zeitouni
Bruno
B
INSERM U900, Institut Curie, Paris, France. svdetect@curie.fr
Boeva
Valentina
V
Janoueix-Lerosey
Isabelle
I
Loeillet
Sophie
S
Legoix-né
Patricia
P
Nicolas
Alain
A
Delattre
Olivier
O
Barillot
Emmanuel
E
D016678:Genome / Q000235:genetics*; D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods*; D012984:Software