Workflow

🧬 Pipeline Workflow

This document describes the analytical workflow implemented in CorGe+.

The pipeline processes sequencing data using a series of modular steps implemented in Nextflow DSL2. Each step is executed independently and automatically parallelized when possible.

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📊 Workflow Overview

The workflow consists of several stages that transform raw sequencing data into interpretable results for genomic surveillance.

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🔬 Pipeline Stages

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 hierarchical-clustering (HC) thresholds.
7. Generate PoODLE manifests.
8. Run MashTree.
9. Generate Microreact files for visual exploration of genomic groups in trees.