VIBES

VIBES annotates prophage sequences and associated bacterial genes and viral proteins to characterize bacteriophage integration events and insertion sites in bacterial genomes.

Key Features:

• Prophage annotation: Identifies and annotates prophage sequences within complete bacterial genomes.
• Bacterial gene and viral protein annotation: Annotates bacterial genes and viral proteins from user-provided genomic data to provide contextual host–phage relationships.
• Insertion site analysis: Detects prophage insertion sites and supports analyses of prophage prevalence across genomes.
• Nextflow workflow: Implemented as a Nextflow-driven workflow to organize pipeline execution.
• Containerized steps: Uses containers for each pipeline step to encapsulate software dependencies and support reproducibility.
• Alignment-based sequence similarity: Employs an alignment-based design that functions as a sequence similarity search manager for general-purpose searches.
• Output formats: Produces results as tab-separated files for downstream data manipulation.
• Visualization generation: Generates interactive visualizations for exploration of prophage annotations and integration patterns.
• Scalability demonstration: Applied to 178 Pseudomonas phage genomes across 1,072 Pseudomonas spp. genomes to illustrate large-scale analysis capability.

Scientific Applications:

• Prophage prevalence studies: Quantifies prophage prevalence across bacterial populations and identifies common insertion hotspots.
• Host–phage integration analysis: Characterizes bacteriophage integration events and their genomic contexts within bacterial chromosomes.
• Impact on host biology: Supports investigation of prophage effects on host fitness and virulence through combined prophage and host gene annotation.
• Comparative genomics: Enables comparative analyses of phage–host interactions across multiple genomes and strains.

Methodology:

VIBES is implemented as a Nextflow-driven, containerized workflow that performs alignment-based sequence similarity searches to annotate prophages, bacterial genes, and viral proteins and outputs tab-separated files and interactive visualizations.