Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in whole bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes and can also be deployed as a general-purpose sequence similarity search manager. VIBES dependencies are managed by containers and execution is managed by Nextflow, minimizing manual setup and operation by users. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072 Pseudomonas spp. genomes. VIBES can be found at https://github.com/TravisWheelerLab/VIBES.

VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes