RSVrecon

RSVrecon processes raw FASTQ files into annotated variant reports and multiple output formats for comprehensive RSV genome assembly, phylogenetic analysis, genotype detection, and clinically relevant mutation reporting.

Key Features:

• Genome Assembly: Reconstructs comprehensive RSV genomes from raw FASTQ files.
• Phylogenetic Analysis: Performs phylogenetic analysis as part of the pipeline workflow.
• Genotype Classification: Detects and classifies RSV genotypes.
• F Protein Mutation Calling: Identifies mutations in the fusion (F) protein, including clinically relevant variations that can reduce vaccination and monoclonal antibody treatment efficacy.
• Variant Reporting: Generates annotated variant reports in multiple formats including CSV, PDF, and HTML.
• Modular Workflow: Implements a scalable and robust workflow using the Nextflow framework.

Scientific Applications:

• RSV Surveillance: Enhances genomic surveillance of Respiratory Syncytial Virus by detecting genetic variations and tracking circulating strains.
• Clinical Research: Translates RSV genomic data into clinically meaningful information to guide clinical care decisions and research.
• Vaccine and Therapeutic Monitoring: Monitors genetic variations in the F protein that may reduce efficacy of vaccination and monoclonal antibody treatments.

Methodology:

RSVrecon is built on the Nextflow framework with a modular design. Benchmarking against existing pipelines was performed using clinical datasets to assess genomic assembly accuracy and functional capabilities.