SVDetect

SVDetect identifies genomic structural variations from paired-end and mate-pair next-generation sequencing data, detecting and localizing insertions, deletions, inversions, duplications, and inter-chromosomal translocations for genomics analyses.

Key Features:

• Detection of Structural Variations: Detects large insertions-deletions (indels), inversions, duplications, and both balanced and unbalanced inter-chromosomal translocations from paired-end and mate-pair reads.
• Sequencing Platform Compatibility: Supports data produced by the Illumina GA and ABI SOLiD platforms.
• Analysis of Anomalous Read Pairs: Analyzes anomalously mapped read pairs provided by current short read aligners.
• Detection Strategies: Implements sliding-window and clustering strategies to localize genomic rearrangements.
• Output Formats: Produces predicted structural variant data in various file formats for integration with other bioinformatics tools and for graphical visualization.

Scientific Applications:

• Cancer Genomics: Enables detection and classification of somatic and germline structural variants relevant to oncogenesis and tumor genome characterization.
• Evolutionary and Comparative Genomics: Supports analysis of chromosomal rearrangements across species to study genome evolution.

Methodology:

Employs sliding-window and clustering strategies to analyze anomalously mapped read pairs provided by short read aligners.