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🧬 CorGe+: Core Genome plus

CorGe+ (“core-gee”) is a bioinformatics pipeline for analyzing bacterial genomes, built to quickly determine genomic linkages and to group related isolates. By combining core genome MLST (cgMLST) and core genome alignment approaches, it provides a scalable way to triage datasets before deeper analysis, making it especially useful for genomic surveillance and outbreak investigations. From a simple sample sheet of FASTA files, CorGe+ produces linkage tables, Microreact-ready visualizations, metadata summaries, and distance-based cluster assignments.

Suggested workflow

Genome assemblies from sequencing pipelines (e.g., PHoeNIx, Bactopia, TheiaProk, or custom workflows) or public databases (e.g., AllTheBacteria, NCBI) can be analyzed with CorGe+ to identify potential linkages and group genetically similar samples. These groupings support more granular analyses for detecting related cases in routine surveillance and outbreak investigations.

Optional downstream analysis with PoODLE enables higher-resolution comparisons within each group, including SNP-based and pangenome analyses.

🌟 Highlights

• 🧬 Fast & scalable: Built for high-throughput screening of large genomic datasets
• 🧪 Multi-species support: Analyzes multiple species in a single run
• 🔗 Linkage detection & grouping: Identifies related samples (alleles or SNPs) and groups them using flexible hierarchical-clustering (HC) thresholds
• 📊 Actionable outputs: Generates CSV reports, Microreact visualizations, and PoODLE-ready sample sheets
• 🗂️ Persistent surveillance database: Automatically compares new samples to historical data. Group nomenclature is preserved when using cgMLST
• 🕒 Metadata-driven insights: Uses ReporTree to summarize genetic clusters across metadata fields (e.g., time, location, clinical data) for enhanced epidemiological interpretation
• ⚙️ Flexible workflows: Supports regrouping, phylogenetic tree generation from prior results, and selective sample removal from the database

📊 Workflow Overview

High-level steps for the default mode:

1. Verify cgMLST schema availability for each species.
2. Perform core genome analysis using ChewBBACA (cgMLST) or Parsnp (core alignment if schema unavailable).
3. Generate a phylogenetic tree with IQ-TREE (optional with --tree).
4. Hierarchical clustering with ReporTree.
5. Create potential linkage tables per species.
6. Select groups per sample using user-defined HC thresholds.
7. Generate PoODLE manifests.
8. Run MashTree.
9. Generate Microreact files for visual exploration of genomic groups in trees.