PathoGFAIR

PathoGFAIR comprises Galaxy-based FAIR workflows that detect and track pathogens from metagenomic Oxford Nanopore sequencing data.

Key Features:

• Metagenomic Pathogen Detection: Employs state-of-the-art tools to detect pathogens at species and subspecies taxonomic ranks from metagenomic Nanopore sequencing data.
• Visualization and Reporting: Incorporates visualizations and reports for comprehensive results presentation.
• Adaptability: Workflows can be applied to metagenomic Nanopore pathogenic data beyond food datasets and adapted for other sequencing techniques.

Scientific Applications:

• Foodborne Pathogen Detection: Detects pathogens in food datasets and traces contamination sources during foodborne outbreak investigations.
• Multi-host Pathogen Surveillance: Successfully tested on samples containing different pathogens from multiple hosts under various experimental conditions.
• Isolation-independent Detection: Detects pathogens regardless of whether the pathogen is isolated or the sample is incubated before sequencing.

Methodology:

Galaxy-based workflows employing state-of-the-art bioinformatics tools; tested on 130 samples with detection evaluated against colony-forming unit and cycle threshold values.