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

BackgroundPangenome variation graphs (PVGs), which represent genomic diversity through multiple genomes alignment, are powerful tools for studying genomic variations in populations. However, current tools often lack integration, efficiency, or require format conversions, to use them, hindering their usability. ResultsHere, we introduce 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. ConclusionsThrough its unified graph manipulation interface, GraTools offers an interesting alternative to the few existing tools for manipulating PVGs, facilitating rapid, efficient and flexible downstream analyses. It is available as an open-source tool (GNU GPLv3), with its documentation available at https://gratools.readthedocs.io.