viroCapt

viroCapt identifies viral insertions in the human genome from next-generation sequencing and directed viral capture data to enable analysis of their roles in cancer pathophysiology.

Key Features:

• Automated Genotyping Phase: Performs a crude genotyping step to select appropriate reference viral genomes for downstream analysis.
• Chimeric Read Identification: Detects chimeric reads that contain both human and viral genetic material to localize candidate integration events.
• Human Sequence Extraction and Mapping: Extracts putative human sequences from chimeric reads and maps them to the human reference genome.
• Candidate Junction Scoring and Ranking: Applies a filtering and ranking algorithm implemented in R to score and prioritize candidate viral–host junctions.
• Data Export and Visualization: Exports results in tabular and visual formats for downstream analysis and interpretation.

Scientific Applications:

• Cancer Research: Enables detection and analysis of viral insertions and preserved oncogenes to investigate viral contributions to oncogenesis.
• Validation on Specific Viruses: Has been validated against published insertion results for human papillomavirus (HPV), hepatitis B virus (HBV), and adeno-associated virus 2 (AAV2).

Methodology:

Integrates bowtie2 for sequence alignment, samtools for sequencing data processing, blat for mapping to the reference genome, extraction of human sequences from chimeric reads, and an R-implemented filtering and ranking algorithm.