Supporting data and scripts produced by the GraTools software

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Supporting data and scripts produced by the GraTools software
Ravel, Sebastien; Marthe, Nina; Carrette, Camille; Mohamed, Mourdas; Sabot, Francois; Christine, Tranchant-Dubreuil, 2026, "Supporting data and scripts produced by the GraTools software", https://doi.org/10.23708/M24LJG, DataSuds, V1
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Description
Here, we introduce GraTools (https://forge.ird.fr/diade/gratools), a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file.
After a one-time graph import, GraTools enables rapid subgraph extraction, fasta sequence retrieval, and comprehensive analyses, including core/dispensable genome ratio calculation or group-specific segment identification. The import step results in conversion in standard data formats (BAM/BED), enabling the reuse of well-optimized existing tools, allowing an efficient storage and the querying of the PVGs large complex data structures. Scalability is ensured by a modular architecture supporting parallel processing and asynchronous I/O operations. GraTools supports coordinates defined on both the primary reference as well as from alternative genomes within the graph without re-importing, and its outputs can be easily visualized or manipulated using external tools.
Using an Asian rice pangenome graph (13 accessions), we demonstrate its ability to easily extract subgraphs, compute depth statistics, and identify subspecies-specific segments. An intuitive command-line interface, a real-time execution feedback and a detailed logging system make this tool suitable for a wide range of applications, from population genetics to breeding and genomic medicine, for both biologists and bioinformaticians. (2026-03-09)
Subject Agricultural Sciences; Computer and Information Science; Medicine, Health and Life Sciences
Keyword Pangenome Variation Graph, Graph-based pangenome analysis, Core and Dispensable Genome
Related Publication GraTools, an user-friendly tool for exploring and manipulating pangenome variation graphs Sébastien Ravel, Nina Marthe, Camille Carrette, Mourdas Mohamed, Francois Sabot, Christine Tranchant-Dubreuil bioRxiv 2025.12.01.691558; doi: https://doi.org/10.64898/2025.12.01.691558 doi: 10.64898/2025.12.01.691558
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gratools_rice_analysis_commands.md
Markdown Text - 33.9 KB
Published Mar 10, 2026
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MD5: 832f5ec934a8604f260043f64937a327
This file provides a complete workflow for analyzing pangenome graphs using GraTools, including example commands, explanations, and use cases from the associated study.
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supporting_data_README.txt
Plain Text - 375 B
Published Mar 10, 2026
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MD5: 0102ef91632371fc7f58d2a6ff2bcbd9
describes the contents of the repository
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get_seglen_frombam.py
additional-scripts/Python Source Code - 3.3 KB
Published Mar 10, 2026
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MD5: a6ba11cdc66e970252bbe35eba20efe0
Script for advanced GraTools pangenome analysis; full details are provided in the included README.
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print_venn_gratools.R
additional-scripts/R Syntax - 947 B
Published Mar 10, 2026
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MD5: fbb59535691dd0dc47ec8f190674e4e1
Script for advanced GraTools pangenome analysis; full details are provided in the included README.
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README
additional-scripts/Plain Text - 2.1 KB
Published Mar 10, 2026
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MD5: 24b9cee6403fbab6f7d945cdee151346
contains information describing each script available in this repository
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script_jap_ind.sh
additional-scripts/Shell Script - 1.0 KB
Published Mar 10, 2026
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MD5: a52ca15e3c8d29b76e4828439be17001
Script for advanced GraTools pangenome analysis; full details are provided in the included README.
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venn_gratools.py
additional-scripts/Python Source Code - 2.8 KB
Published Mar 10, 2026
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MD5: c94ce2c9d8b8d36108bb1f1f41e19704
Script for advanced GraTools pangenome analysis; full details are provided in the included README.
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gratools_core_dispensable_ratio_white.png
gratools_core_dispensable_ratio_white.png
screenshots/PNG Image - 98.8 KB
Published Mar 10, 2026
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MD5: c52a96e1a3a1c1fcfe49399c5030fc86
Screenshots showing tabulated outputs of several GraTools commands, displaying structured tables with color-coded formatting for improved readability.
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gratools_depth_nodes_stat_white.png
gratools_depth_nodes_stat_white.png
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Published Mar 10, 2026
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MD5: 8a9f04f9ac34ae48143f1ec262218df2
Screenshots showing tabulated outputs of several GraTools commands, displaying structured tables with color-coded formatting for improved readability.
Documentation
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gratools_stats_white.png
gratools_stats_white.png
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Published Mar 10, 2026
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MD5: e8eeed32f3adcea3d7e0cd1e6f805e96
Screenshots showing tabulated outputs of several GraTools commands, displaying structured tables with color-coded formatting for improved readability.
Documentation
Preview "screenshots/gratools_stats_white.png"
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