Seeksv

Seeksv detects somatic structural variations and virus integration events in the human genome to support analysis of cancer-related genomic alterations and viral oncogenesis.

Key Features:

• Detection Capabilities: Identifies deletions (DEL), insertions, inversions, and inter-chromosome transfers with single-nucleotide resolution breakpoints.
• Data Compatibility: Processes single-end and paired-end sequencing reads.
• Signal Utilization: Integrates split read, discordant paired-end read, read depth, and fragments with both ends unmapped signals for structural variation detection.
• Homology Region Handling: Employs a rescue model to detect SVs in regions of sequence homology.
• Implementation: Implemented in C++ for scalable performance on large genomic datasets.
• Performance Evaluation: Empirical evaluations on simulated and real datasets report superior efficiency and precision, with hepatitis B virus integration experiments showing over 90% true positive verification.

Scientific Applications:

• Cancer Research: Identification of somatic structural variations that can alter tumor-related gene expression and contribute to cell proliferation and tumor formation.
• Viral Oncogenesis: Detection of virus integration sites to study genomic instability and viral-driven transformation of normal cells into tumor cells, including hepatitis B virus integration analysis.

Methodology:

Simultaneous analysis of split reads, discordant paired-end reads, read depth variations, and fragments with both ends unmapped, combined with a rescue model to recover SVs in homologous regions.