GraTools: a powerful tool for analyzing pangenome graphs

What’s GraTools ?

GraTools offered a set of commands for analyzing and handling pangenome graphs quickly, whatever the model and therefore the size and the complexity of the GFA file.

For example, GraTools allows to extract sequences or subgraphs, convert graphs into FASTA sequences, and identify shared and specific nodes across samples. Additionally, it provides essential statistics for chromosomes and samples data. With multi-threading support and flexible logging capabilities, GraTools is an efficient solution for pangenome graph analysis.

GraTools has been developed by IRD and CIRAD, as part of a collaboration between the PANEEC/DIADE and PHIM research teams.

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

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

How to use GraTools commands ?

GraTools is composed of multiple commands that can be invoked according the following syntax:

GraTools [command] [options]

For example, to list the chromosomes per sample in a GFA file

GraTools show_chr --gfa graph.gfa --full

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
      • configure_logger()
    • update_logger_file_suffix
      • update_logger_file_suffix()
    • validate_percentage_or_int
      • validate_percentage_or_int()
  • Classes
    • AsyncGfaDatabase
      • AsyncGfaDatabase
    • SubGraph
      • SubGraph
    • GFA
      • GFA
    • GratoolsBam
      • GratoolsBam
    • ThreadedRichHandler
      • ThreadedRichHandler
    • CustomCommand
      • CustomCommand
    • CustomGroup
      • CustomGroup

Indices and tables

• Index

• Module Index

• Search Page

License

GraTools is freely available under the [GNU General Public License, version 3 (GPLv3)](https://www.gnu.org/licenses/gpl-3.0.en.html).

Intellectual property belongs to IRD , CIRAD and previously cited authors.

Authors

• 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

Thanks to Cécile Triay for the logo. Thanks to the i-trop plateform, especially Ndomassi Tando, for the support.

Contact

If you have questions, requests, or bug reports, please contact to the GraTools mailing list : [gratools@ird.fr](mailto:gratools@ird.fr)