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. It also 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 is developed at IRD and CIRAD within the PANEEC/DIADE and PHIM teams.

Quick Start Guide

• Install GraTools
• Getting commands list and help
• Using GraTools
  • list_chr
  • list_samples
  • get_fasta
  • extract_sub_graph
  • core_dispensable_ratio
  • get_segment_by_depth
  • depth_nodes_stat
• 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 subcommands
• gratools index
  • Options
  • Usage Examples
• gratools stats
  • Options
  • Usage Examples
  • Stats explained
    • Graph Stats
    • Segment Stats
    • Bins (Segment Length)
    • Similarity & Depth
    • Links Stats
    • Graph Structure
• gratools list_samples
  • Options
  • Usage Examples
• gratools list_chr
  • Options
  • Usage Examples
• gratools extract_sub_graph
  • 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
  • GFA exemple of merge option
• 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 sequence 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_segment_by_depth
  • Options
  • Usage Examples
    • List nodes shared between percentages or numbers of individuals
  • Illustrated Example
• gratools depth_nodes_stat
  • Options
  • Usage Examples
    • Display statistics about the node detph
• gratools specific_and_shared_segments
• gratools shell_completion
  • Options
  • Usage Examples

Gratools for developers

• gratools Package
  • gratools.Graph Module
  • gratools.gratools Module
  • gratools.logger_config Module
  • gratools.main Module

Indices and tables

• Index

• Module Index

• Search Page

License

GraTools is freely avalaible under a GLPL license (Version 3).

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.

Mailing list

If you have questions, requests, or bugs to report, please email to the gratools mailing list