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Quick Start Guide

  • 🚀 Quick Start Guide
    • 📦 Installation
    • 🛠️ Command Overview
    • 📖 Command Examples
    • 🔄 Typical Workflow
    • 🧪 Testing GraTools
    • ⚠️ Troubleshooting
    • 🆘 Further Assistance

Advanced Usage

  • All commands
    • 🚀 CLI Overview
    • 📚 Command Reference
      • Core Operations
      • GFA Content Information
      • GFA Data Extraction
      • GFA Pangenome Analysis
  • index
    • Options
    • Usage Examples
    • What happens during Indexing?
  • stats
    • Options
    • Usage Examples
    • Metrics Explained
  • list_samples
    • Options
    • Usage Example
  • list_chr
    • Options
    • Usage Examples
    • Output Formats Explained
  • extract_subgraph
    • Options
    • Usage Examples
    • Illustrated Process
    • The --merge-dist Parameter
  • get_fasta
    • Options
    • Usage Examples
    • Illustrated Process
  • core_dispensable_ratio
    • Options
    • Usage Example
    • Understanding the Results
    • Process & Logic
  • get_segment_by_depth
    • Options
    • Illustrated Use Cases
      • Rare Segments Extraction
      • Core Segments Extraction
    • Logic & Parameters
  • depth_nodes_stat
    • Options
    • Usage Example
    • Understanding the Table
  • specific_groups_sample
    • Options
    • Complete Usage Example
      • Step 1: Prepare Input Lists
      • Step 2: Run Analysis
      • Step 3: Review Results
    • 📂 Output Files Detail
    • Visual Logic
  • shell_completion
    • Options
    • 🚀 Setup Instructions
      • Step 1: Generate the Script
      • Step 2: Configure your Shell
      • Step 3: Reload Configuration
    • 🎮 How to Use it

GraTools for developers

  • Developer API Reference
    • 🚀 Quick Navigation
    • 🏗️ Core Graph Engine
    • 📊 Analysis & Extraction
    • 🚀 System & CLI
    • 🛠️ Other Commands & Utilities
    • 💡 Development Guide
    • 🛠️ Implementation Example
    • 📚 Project Resources
GraTools
  • Overview: module code

All modules for which code is available

  • gratools.Graph
  • gratools.Gratools
  • gratools.gfa_extract
  • gratools.logger_config
  • gratools.useful_function

© Copyright 2024–2026, Sebastien Ravel (PHIM, CIRAD), Christine Tranchant-Dubreuil (DIADE, IRD), Camille Carrette (DIADE, IRD/SYNGENTA), Nina Marthe (DIADE, IRD), Mohamed Mourdas (DIADE, IRD), François Sabot (DIADE, IRD).