GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph

AbstractThe increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic information from multiple genomes, offer thus a more comprehensive representation of intraspecific diversity. However, pangenomes in form of graph often lack annotation information, which limits their utility for forward analyses. We introduce here GrAnnoT, a tool designed for efficient and reliable annotation transfer using such graphs, by projecting existing annotations from a source genome to the graph and subsequently to other embedded genomes. GrAnnoT was benchmarked against state-of-the-art tools on pangenome graphs and linear genomes from rice, human, andE. coli. The results demonstrate that GrAnnoT is consensual, conservative, and fast, outperforming alignment-based methods in accuracy or speed or both. It provides informative outputs, such as presence-absence matrices for genes, and alignments of transferred features between source and target genomes, aiding in the study of genomic variations and evolution. GrAnnoT’s robustness and replicability across different species make it a valuable tool for enhancing pangenome analyses. GrAnnoT is available under the GNU GPLv3 licence athttps://forge.ird.fr/diade/dynadiv/grannot.