GraTools 1.0.0

GraTools is a powerful and efficient toolkit for working with pangenome graphs,

GraTools is a powerful tool for analyzing and handling pangenome graphs quickly, whatever the model and therefore the size and the complexity of the GFA file.

It allows users 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.

Documentation

https://gratools.readthedocs.io/en/latest/

Install GraTools

GraTools can be installed like any standard Python package. For a quick start, please refer to the quick start guide in the official documentation.

Using GraTools

Gratools is composed of multiple commands that can be used with the following syntax:

gratools [command] [options]

To view the list of available commands and their descriptions, simply run:

gratools

This will display all the commands supported by Gratools.

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

gratools show_chr --gfa graph.gfa --full

For more details, refer to the For more details, refer to the Quick Start section or the full command manual in the official documentation. or the full command manual in the official documentation.

Test GraTools with a GFA file

wget http://itrop.ird.fr/GraTools/data-gratools.tar.gz
tar -zxvf data-gratools.tar.gz

Discovering GraSuite

GraTools is one of the tools in GraSuite, a comprehensive ecosystem of tools for working with GFA pangenome graphs — from creation to analysis and visualization.

Citation

https://forge.ird.fr/diade/gratools

Maintainer

• Sébastien RAVEL (PHIM, CIRAD), [e-mail]

• Christine TRANCHANT (DIADE, IRD), [e-mail]

Authors

• Sébastien RAVEL (PHIM, CIRAD)

• Camille CARRETTE (PANEEC/DIADE, IRD/SYNGENTA)

• Nina MARTHE (PANEEC/DIADE, IRD)

• Mohamed MOURDAS (PANEEC/DIADE, IRD)

• François SABOT (PANEEC/DIADE, IRD)

• Christine TRANCHANT (PANEEC/DIADE, IRD)

Thanks

• Cécile Triay for the logo.

• the i-trop plateform, especially Ndomassi Tando, for the support.

License

Licensed under GLPLv3.

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