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
GraTools
Overview: module code
All modules for which code is available
gratools.Graph
gratools.Gratools
gratools.gfa_extract
gratools.logger_config
gratools.useful_function