ViralFusionSeq

ViralFusionSeq detects viral integration events and viral–human fusion transcripts from RNA-Seq and DNA-Seq data to map insertional mutagenesis and fusion products relevant to virus-induced oncogenesis.

Key Features:

• Integration of Multiple Analytical Approaches: Combines soft-clipping information, read-pair analysis, and targeted de novo assembly to enhance detection of viral integration sites and expressed viral fusion events within host genomes.
• High Sensitivity and Accuracy: Validated on RNA-Seq experiments, simulated DNA-Seq experiments, and re-analysis of published DNA-Seq datasets with demonstrated sensitivity and accuracy in identifying viral-human fusions.
• Comprehensive Annotation Capabilities: Provides detailed annotation of discovered viral integration sites and fusion transcripts to support biological interpretation.

Scientific Applications:

• Insertional Mutagenesis Mapping: Maps viral integration locations in the human genome to study insertional mutagenesis resulting from virus infections.
• Fusion Transcript Discovery: Identifies expressed viral-human fusion transcripts from RNA-Seq data.
• Study of Virus-Induced Oncogenesis: Supports investigation of molecular mechanisms underlying virus-induced cancers by linking integration sites and fusion transcripts to genomic context.

Methodology:

Utilizes soft-clipped reads, read-pair discordant alignment analysis, and targeted de novo assembly focused on candidate regions to detect and reconstruct viral integration sites and fusion transcripts.