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GrAuFlow: A snakemake workflow for pangenome graph augmentation using short read data

hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
hal.structure.identifierUniversité de Rouen Normandie [UNIROUEN]
dc.contributor.authorMALET, Antoine
hal.structure.identifierInstitut de Génétique, Environnement et Protection des Plantes [IGEPP]
dc.contributor.authorLEGEAI, Fabrice
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUVAUX, Ludovic
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
dc.contributor.authorFOURNIER, Elisabeth
hal.structure.identifierPlant Health Institute of Montpellier [UMR PHIM]
dc.contributor.authorGLADIEUX, Pierre
hal.structure.identifierEidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] [ETH Zürich]
dc.contributor.authorLORRAIN, Cécile
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorLEBRUN, Marc-Henri
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorGENISSEL, Anne
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorMARCEL, Thierry
hal.structure.identifierBIOlogie et GEstion des Risques en agriculture [BIOGER]
dc.contributor.authorLAPALU, Nicolas
dc.date.conference2025-07-08
dc.description.abstractEnPangenome graphs are gaining popularity in genomic analysis as they address the bias introduced by using a single reference genome in population variant analyses. However, with the constant acquisition of new sequencing data, it is essential to update these graphs to incorporate new genomic resources. When new fully sequenced genomes are available, reconstructing the graph is often the most convenient method. In the case of small sequences, such as those from amplicon sequencing, augmenting the graph may be more straightforward, as only a small portion of the graph will be modified. In this study, we are interested in augmenting a graph with fragmented genomes assembled from short reads. This data represents a valuable resource of genetic diversity that is not currently utilized in graphs, where use of T2T genomes are recommended.In this context, we are developing a workflow called GrAuFlow (Graph Augmentation Workflow) using the Snakemake workflow manager (Mölder et al, 2021). First, GrAuFlow performs an assembly of Illumina short read data using the SPAdes assembly toolkit ( Prjibelski et al, 2020), retaining only contigs that pass stringent quality filters. Then, contigs are fractioned in long reads sequence like and mapped onto the graph using different tools: Palss (Denti et al, 2025) , GraphAligner ( Rautiainen et al, 2020) and SVArp (Soylev et al, 2024), before graph augmentation with vg augment (Garrison etal, 2018). GrAuFlow then extracts structural variants (SV) from the different strategies to retain only well supported with a minimal length. Finally, SVs are compared to modify the graph only with those that show consistent variants across all graph augmentation tools. To test our approach, we use Zymoseptoria tritici, a fungal pathogen responsible for septoria tritici blotch of wheat.Based on graphs generated by Minigraph and Minigraph-Cactus using 8 genomes of Zymoseptoria tritici, we validate that short-reads data could be useful to add new information in pangenome graph. Nevertheless, this approach is limited to medium-size variants. Structural variants that are not easilyassembled due to repeat contents or complex events may not be detected, which makes this approach interesting for enriching specific loci of interest.
dc.language.isoen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enSnakemake pipeline
dc.subject.enZymoseptoria tritici
dc.subject.enPangenome graph
dc.title.enGrAuFlow: A snakemake workflow for pangenome graph augmentation using short read data
dc.typeAutre communication scientifique (congrès sans actes - poster - séminaire...)
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.conference.titleJournées Ouvertes Biologie, Informatique, Mathématiques (JOBIM2025)
bordeaux.countryFR
bordeaux.conference.cityBordeaux
bordeaux.peerReviewedoui
hal.identifierhal-05209521
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.organizerSFBI
hal.conference.organizerIFB
hal.conference.organizerGDR BIMMM
hal.conference.end2025-07-11
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05209521v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=MALET,%20Antoine&LEGEAI,%20Fabrice&DUVAUX,%20Ludovic&FOURNIER,%20Elisabeth&GLADIEUX,%20Pierre&rft.genre=conference


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