Dubreuil Tranchant Christine auteur aut IRD Chenal Clothilde auteur aut IRD Blaison M. auteur aut IRD Albar Laurence auteur aut IRD Klein V. auteur aut IRD Mariac Cédric auteur aut IRD Wing R.A. auteur aut IRD Vigouroux Yves auteur aut IRD Sabot François auteur aut IRD text journalArticle eng text/pdf reformatted digital access We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection. specialized 084 076 122 5 1 lqad013 [8 ] 2023 2631-9268 https://www.documentation.ird.fr/hor/fdi:010090913 10.1093/nargab/lqad013 2631-9268 [F B010090913] https://www.documentation.ird.fr/hor/fdi:010090913 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2024-07/010090913.pdf IRD - Base Horizon / Pleins textes 2024-05-22 2025-02-24 fdi:010090913 fre