GraTools Logo

Quick Start Guide

  • Install GraTools
    • Install the lastest GraTools release (Recommended)
    • Install the development version from github
    • Verify the installation
  • Command List and Help
  • Using GraTools
    • stats
    • list_samples
    • list_chr
    • extract_subgraph
    • get_fasta
    • core_dispensable_ratio
    • get_segments_by_depth
    • depth_nodes_stat
    • specific_groups_sample
  • Typical Workflow
  • Testing GraTools
  • Troubleshooting
  • Further Assistance

Advanced Usage

  • GraTools: A Pangenome GFA Toolkit
    • Available Subcommands
    • Command Reference
  • gratools index
    • Options
    • Usage Examples
    • What index Does
  • gratools stats
    • Options
    • Usage Examples
    • Stats Explained
      • Graph Overview
      • Segment Statistics
      • Link Statistics
      • Path (Walk) Statistics
      • Segment Sharing & Depth
      • Graph Structure
  • gratools list_samples
    • Options
    • Usage Examples
  • gratools list_chr
    • Options
    • Usage Examples
  • gratools extract_subgraph
    • Options
    • Usage Examples
      • Extracting a subgraph for a specific region
      • Extracting a subgraph for a specific region and generate a FASTA file from the subgraph
      • Extracting a subgraph for a list of samples provided in a file
    • Illustrated Example
    • The –merge-dist Option Explained
  • gratools get_fasta
    • Options
    • Usage Examples
      • Extracting a sequence for a specific sample and region
      • Extracting sequences for all samples included in the graph
      • Extracting sequences for a list of samples provided in a file
    • Illustrated Example
  • gratools core_dispensable_ratio
    • Options
    • Usage Examples
      • Displays the ratio of core and dispensable segments
    • Illustrated Example
  • gratools get_segments_by_depth
    • Options
    • Usage Examples
      • List segments shared by a number of individuals and save to a file
      • List core segments (by percentage) and display them in the terminal
    • Illustrated Example
  • gratools depth_nodes_stat
    • Options
    • Usage Examples
      • Display statistics about the node depth
  • gratools specific_groups_sample
    • Options
    • Complete Usage Example
    • Illustrated Example
  • gratools shell_completion
    • Introduction
    • Options
    • Setup Instructions
    • How to Use Shell Completion

GraTools for developers

  • gratools Package
    • Functions
      • configure_logger
      • update_logger_file_suffix
      • validate_percentage_or_int
    • Classes
      • AsyncGfaDatabase
      • SubGraph
      • GFA
      • GratoolsBam
      • ThreadedRichHandler
      • CustomCommand
      • CustomGroup
GraTools
  • Search

© Copyright 2024–2025, 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).