HI-FEVER

HI-FEVER automates the high-throughput discovery and annotation of endogenous viral elements (EVEs) in eukaryotic host genomes through a parallelizable and customizable Nextflow workflow.

Key Features:

• High-throughput EVE discovery: Scales to handle millions of viral protein queries across multiple host genomes.
• Parallelizable architecture: Executes efficiently on both laptops and high-performance computing nodes.
• Customizable parameters: Allows researchers to fine-tune parameters to their specific research needs.
• Comprehensive EVE annotation: Generates detailed annotations of discovered EVEs to provide evolutionary insights.

Scientific Applications:

• Paleovirology research: Addresses computational and biological challenges in detecting endogenous viral elements.
• Virus-host evolution studies: Provides insights into virus and host evolutionary history through EVE analysis.
• Comparative genomics: Enables screening of multiple host genomes against extensive viral protein databases.

Methodology:

The pipeline is implemented in Nextflow and supports Pixi environment compatibility with Conda and Apptainer containerization.