VariationHunter

VariationHunter detects structural rearrangements, specifically deletions, insertions, and inversions greater than 5 kilobases, in whole-genome shotgun and paired-end sequencing data from NGS (Illumina, 454 Life Sciences, ABI SOLiD) and capillary sequencing to identify large structural variants in genomes.

Key Features:

• Combinatorial Formulations: Employs combinatorial formulations to detect structural variations between a reference genome and whole-genome shotgun- or paired-end-sequenced data.
• Algorithmic Efficiency and Reliability: Implements efficient, tailored algorithms for each combinatorial formulation to enable fast and accurate detection of structural variants in short-read, error-prone NGS data.
• Broad Applicability: Processes data from Illumina, 454 Life Sciences, ABI SOLiD and capillary sequencing technologies and applies to studies involving cancer and other disease-associated genomic variation.

Scientific Applications:

• Human Genome Structural Variation Project: Identification and classification of structural variants among normal individuals using ultra-high-throughput sequencing data.
• Disease-associated variant discovery: Detection of large deletions, insertions, and inversions relevant to cancer and other diseases linked to genomic variation.
• Population-scale genomic variation analysis: Comparative analysis across numerous individual genomes to characterize genomic diversity.

Methodology:

Uses paired-end sequencing (including fosmid-based approaches), combinatorial formulations, and tailored algorithms designed to accommodate short read lengths and sequencing errors in NGS and capillary data.