Complete pangenome graph annotation with GrAnnoT and GrAPEx

Abstract

Background: Pangenome variations graphs (PVG) are promising structures to study diversity and reduce reference bias in genomics. However, it is not currently possible include complete annotation of the PVG. In a previous work, we introduced GrAnnoT, a tool for transferring the annotation from a reference genome to a PVG, and from a PVG to its embedded genomes. However, GrAnnoT was limited to transferring one annotation to the graph, and thus could not include all genes. Results: We implemented new options to GrAnnoT, that can now handle annotations of multiple genomes, and integrate them in the graph. We also developed GrAPEx, a pipeline that identifies, extracts and annotates non-annotated regions in the graph. We tested those two tools to attest their performances. Our benchmarks revealed that both GrAnnoT and GrAPEx are reliable. GrAnnoT is now able to integrate correctly several annotations, increasing the amount of biological information available in the graph. Additionally, it offers useful options to study gene distribution in the PVG. GrAPEx allows rapid annotation of the whole PVG, with no reduction in the annotation quality. Conclusion: Overall, the two tools presented here allow to annotate thoroughly the whole PVG, and integrate biological annotation to the pangenome. It also reduces the previous reference bias, where only one annotation (often the reference one) could be included in the graph. This constitutes a precious addition to the pangenomic toolkit.