ReporTree

ReporTree: Genomics-Informed Pathogen Cluster Analysis Pipeline

ReporTree automates identification, characterization, and longitudinal tracking of pathogen genetic clusters from phylogenetic trees and associated metadata to support genomics-informed surveillance.

Key Features:

• Automated Cluster Identification: Detects and characterizes genetic clusters across user-defined distance thresholds or cluster stability regions.
• Metadata Integration: Integrates epidemiological metadata, including timespan, geography, vaccination status, clinical data, and antibiotic resistance, into surveillance-oriented reports.
• Hierarchical Cluster Nomenclature: Maintains consistent cluster naming across analyses using a hierarchical coding system combining multi-level information.
• Multi-Workflow Compatibility: Supports multiple input formats and clustering methods, including cgMLST and wgMLST workflows and alignment-based SNP workflows.
• Benchmark Validation: Validated on foodborne bacterial pathogens using cg/wgMLST, Mycobacterium tuberculosis using alignment-based SNP analysis, and Neisseria gonorrhoeae for genogroup identification.

Scientific Applications:

• Routine Genomic Surveillance: Enables reproducible detection and monitoring of pathogen genetic clusters across datasets.
• Outbreak Detection: Identifies and contextualizes emerging clusters using integrated genomic and epidemiological data.
• Cross-Species Surveillance: Applied to diverse pathogens including SARS-CoV-2 and Listeria monocytogenes.

Methodology:

Processes phylogenetic trees and associated metadata to define genetic clusters based on distance thresholds or stability regions, integrates hierarchical coding for longitudinal tracking, and supports cgMLST, wgMLST, and alignment-based SNP analytical workflows.