@article{fdi:010096014,
  title = {{G}r{A}nno{T}, a tool for efficient and reliable annotation transfer through pangenome graph},
  author = {{M}arthe, {N}ina and {Z}ytnicki, {M}. and {S}abot, {F}ran{\c{c}}ois},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. {P}angenomes, encompassing the genomic information from multiple genomes, thus offer a more comprehensive representation of intraspecific diversity. {H}owever, pangenomes in form of a variation graph often lack annotation information and tools for manipulating it, which limits their utility for downstream analyses. {W}e introduce here {G}r{A}nno{T}, a tool designed for an efficient and reliable integration of annotation information in such variation graphs. {I}t projects existing annotations from a source genome to the variation graph and subsequently to other embedded genomes. {G}r{A}nno{T} was benchmarked against state-ofthe-art tools on pangenome variation graphs and linear genomes from {A}sian rice, and tested on human and {E}. coli data. {T}he results demonstrate that {G}r{A}nno{T} is consensual, conservative, and fast. {I}t provides informative outputs, such as presence-absence matrices for genes, and alignments of transferred features between source and target genomes, helping in the study of genomic variations and evolution. {G}r{A}nno{T}'s robustness and replicability across different species make it a valuable tool for enhancing pangenome analyses. {G}r{A}nno{T} is available under the {GNU} {GPL}v3 licence at https://forge.ird.fr/diade/dynadiv/grannot.},
  keywords = {},
  booktitle = {},
  journal = {{PEER} {C}ommunity {J}ournal},
  volume = {5},
  numero = {},
  pages = {e133 [31 p.]},
  year = {2025},
  DOI = {10.24072/pcjournal.651},
  URL = {https://www.documentation.ird.fr/hor/fdi:010096014},
}