a powerful tool for analyzing pangenome graphs

Analyze and handle pangenome graphs quickly, whatever the model, size, or complexity.

🚀 High Performance

Multi-threading support for fast analysis of large GFA files, regardless of model complexity.

🛠️ Versatile Toolkit

Extract sequences, subgraphs, convert to FASTA, and identify shared/specific nodes.

📊 Deep Statistics

Generate essential statistics for chromosomes, samples, and core/dispensable ratios.

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What’s GraTools?

GraTools offers a set of commands designed for rapid analysis of pangenome graphs. It provides an efficient solution for researchers to explore GFA files, providing insights into genome structure and sample relationships.

Developed by IRD and CIRAD, as part of a collaboration between the PANEEC/DIADE and PHIM research teams.

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🚀 Quick Start Guide

This guide will help you get up and running with GraTools in no time.

🚀 Quick Start Guide

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📖 Advanced Usage

Explore the full potential of GraTools with detailed command documentation.

View Commands

💻 For Developers

Access the module documentation and API details for integration.

Module API

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Usage Syntax

GraTools follows a simple command-line interface:

GraTools [command] [options]

Example: List chromosomes per sample in a GFA file:

GraTools show_chr --gfa graph.gfa --full

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📑 Documentation Navigation

Quick Start Guide

• 🚀 Quick Start Guide
  • 📦 Installation
  • ✅ Verification
  • 🛠️ 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
• import
  • Options
  • Usage Examples
  • What happens during importing?
• stats
  • Options
  • Usage Examples
  • Metrics Explained
• list_samples
  • Options
  • Usage Example
• list_chr
  • Options
  • Usage Examples
  • Output Formats Explained
• get_subgraph
  • Options
  • Usage Examples
  • Illustrated Process
  • The --merge-dist Parameter
  • Overview of merge-dist settings
  • Concrete Example: Query Region 45–100 (55bp span)
  • Observation Summary
  • When to Use Each Setting
  • Impact on Subgraph Size
• get_fasta
  • Options
  • Usage Examples
  • Illustrated Process
• pan_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

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Authors & Acknowledgments

👥 Development Team

• Sébastien RAVEL (PHIM, CIRAD)

• Camille CARRETTE (DIADE, IRD/SYNGENTA)

• Nina MARTHE (DIADE, IRD)

• Mohamed MOURDAS (DIADE, IRD)

• François SABOT (DIADE, IRD)

• Christine TRANCHANT (DIADE, IRD)

🤝 Acknowledgments & Contact

• Logo: Cécile Triay.

• Support: i-trop plateform (Ndomassi Tando).

• Mailing list: gratools@ird.fr

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License

⚖️ GPLv3 License

GraTools is freely available under the GNU General Public License, version 3 (GPLv3). Intellectual property belongs to IRD and CIRAD.

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Indices and tables

• Index

• Module Index

• Search Page