Work

GraTools, a user-friendly tool for exploring and manipulating pangenome variation graphs

Year: 2026

Type: article

Abstract: Background Pangenome variation graphs (PVGs) are powerful tools for studying genomic variations in populations, as they represent genomic diversity through multiple genome alignments. However, current tools often lack integration and efficiency, and require format conversions to be used, which hinders their usability. Results Here, we introduce GraTools, a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file, which is part of the GraSuite [1]. After a one-time graph import, GraTools enables the rapid extraction of subgraphs, retrieval of FASTA sequences, and the performance of comprehensive analyses, including the calculation of the core/dispensable genome ratio or the identification of group-specific segments. Importing the data results in conversion to standard formats (BAM/BED), enabling the reuse of well-optimised existing tools and allowing efficient storage and querying of large, complex PVG data structures. Scalability is ensured by a modular architecture that supports parallel processing and asynchronous I/O operations. GraTools supports coordinates defined on the primary reference and alternative genomes within the graph without re-import, and its outputs can be easily visualised or manipulated using external tools. Using an Asian rice pangenome graph comprising 13 accessions, we demonstrate GraTools' ability to easily extract subgraphs, compute depth statistics and identify subspecies-specific segments. Its intuitive command-line interface, real-time execution feedback, and detailed logging system make this tool suitable for a wide range of applications, from population genetics to breeding and genomic medicine, for biologists and bioinformaticians alike. Conclusions Through its unified graph manipulation interface, GraTools offers an interesting alternative to existing tools for manipulating PVGs, facilitating rapid, efficient, and flexible downstream analyses. GraTools is available as an open-source tool (GNU GPLv3), and its documentation can be found at https://gratools.readthedocs.io .

Source: BMC Bioinformatics

DOI: 10.1186/s12859-026-06657-z

Authors: Sebastien Ravel, Nina Marthe, Camille Carrette, Mourdas Mohamed, Francois Sabot, Christine Tranchant-Dubreuil