VirPipe

VirPipe detects and analyzes viral genomes from Nanopore and Illumina sequencing data to support identification and analysis of viral sequences.

Key Features:

• Sequencing compatibility: Supports Nanopore and Illumina sequencing data as input for viral genome detection and analysis.
• Viral detection and analysis: Integrates computational steps for identification and analysis of viral sequences from raw sequencing reads.
• Customization options: Provides configurable parameters to adapt processing to different experimental designs and datasets.
• High-throughput data handling: Designed to process large datasets typical of high-throughput sequencing while maintaining detection accuracy.
• Implementation technologies: Implemented using Python and Nextflow for workflow management.

Scientific Applications:

• Outbreak surveillance: Detection of viral genomes from sequencing data to support pathogen surveillance during outbreaks.
• Epidemiological investigations: Identification of viral sequences to inform epidemiological studies and transmission analyses.
• Real-time monitoring: Enables real-time analysis and monitoring using Nanopore sequencing for rapid detection and monitoring of viruses.

Methodology:

The pipeline integrates various bioinformatics tools and algorithms to process raw Nanopore and Illumina sequencing data, identify viral sequences, and analyze them, and is designed to handle large high-throughput datasets.