a powerful tool for analyzing pangenome graphsο
Analyze and handle pangenome graphs quickly, whatever the model, size, or complexity.
Multi-threading support for fast analysis of large GFA files, regardless of model complexity.
Extract sequences, subgraphs, convert to FASTA, and identify shared/specific nodes.
Generate essential statistics for chromosomes, samples, and core/dispensable ratios.
β
Whatβs GraTools?ο
GraTools offers a set of commands designed for rapid analysis of pangenome graphs. It provides an efficient solution for researchers to explore GFA files, providing insights into genome structure and sample relationships.
Developed by IRD and CIRAD, as part of a collaboration between the PANEEC/DIADE and PHIM research teams.
β
This guide will help you get up and running with GraTools in no time.
β
Explore the content of a PVG: basic statistics, sample listing,
and chromosome/contig inventory using stats, list_samples and list_chr.
Extract a subgraph or FASTA sequences for any genomic locus, using coordinates from any embedded haplotype β no re-indexing required.
Compute the core vs. dispensable genome ratio and identify nodes
specific to one group of samples compared to another with pan_ratio and groups.
Power-user workflow: compute subspecies-specific pangenome sizes in bp
by combining groups output with the GraTools BAM file via the pysam API.
β
Explore the full potential of GraTools with detailed command documentation.
Access the module documentation and API details for integration.
β
Usage Syntaxο
GraTools follows a simple command-line interface:
GraTools [command] [options]
Example: List chromosomes per sample in a GFA file:
GraTools show_chr --gfa graph.gfa --full
β
π Documentation Navigation
Quick Start Guide
Use Cases
Advanced Usage
GraTools for developers
References
β
Licenseο
GraTools is freely available under the GNU General Public License, version 3 (GPLv3). Intellectual property belongs to IRD and CIRAD.
β