Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection
hal.structure.identifier | Université de Liège - Gembloux | |
dc.contributor.author | TAMISIER, Lucie | |
hal.structure.identifier | Research Institute for Agricultural, Fisheries and Food [ILVO] | |
dc.contributor.author | HAEGEMAN, Annelies | |
hal.structure.identifier | Research Institute for Agricultural, Fisheries and Food [ILVO] | |
dc.contributor.author | FOUCART, Yoika | |
hal.structure.identifier | Université de Liège - Gembloux | |
dc.contributor.author | FOUILLIEN, Nicolas | |
hal.structure.identifier | University of California [Davis] [UC Davis] | |
dc.contributor.author | AL RWAHNIH, Maher | |
hal.structure.identifier | University of Sütçü Imam | |
dc.contributor.author | BUZKAN, Nihal | |
hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
dc.contributor.author | CANDRESSE, Thierry | |
hal.structure.identifier | CNR Istituto per la Protezione Sostenibile delle Piante [Torino, Italia] [IPSP] | |
dc.contributor.author | CHIUMENTI, Michela | |
hal.structure.identifier | Research Institute for Agricultural, Fisheries and Food [ILVO] | |
dc.contributor.author | DE JONGHE, Kris | |
hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
dc.contributor.author | LEFEBVRE, Marie | |
hal.structure.identifier | Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ] | |
dc.contributor.author | MARGARIA, Paolo | |
hal.structure.identifier | Agroscope | |
dc.contributor.author | SÉBASTIEN REYNARD, Jean | |
hal.structure.identifier | University of California [Davis] [UC Davis] | |
dc.contributor.author | STEVENS, Kristian | |
hal.structure.identifier | National Institute of Biology [Ljubljana] [NIB] | |
dc.contributor.author | KUTNJAK, Denis | |
hal.structure.identifier | Université de Liège - Gembloux | |
dc.contributor.author | MASSART, Sébastien | |
dc.date.issued | 2021-04-02 | |
dc.description.abstractEn | The widespread use of High-Throughput Sequencing (HTS) for detection of plant viruses and sequencing of plant virus genomes has led to the generation of large amounts of data and of bioinformatics challenges to process them. Many bioinformatics pipelines for virus detection are available, making the choice of a suitable one difficult. A robust benchmarking is needed for the unbiased comparison of the pipelines, but there is currently a lack of reference datasets that could be used for this purpose. We present 7 semi-artificial datasets composed of real RNA-seq datasets from virus-infected plants spiked with artificial virus reads. Each dataset addresses challenges that could prevent virus detection. We also present 3 real datasets showing a challenging virus composition as well as 8 completely artificial datasets to test haplotype reconstruction software. With these datasets that address several diagnostic challenges, we hope to encourage virologists, diagnosticians and bioinformaticians to evaluate and benchmark their pipeline(s). | |
dc.language.iso | en | |
dc.subject.en | High-Throughput Sequencing | |
dc.subject.en | Reference data | |
dc.subject.en | Semi-artificial dataset | |
dc.subject.en | Plant virus detection | |
dc.subject.en | Bioinformatics pipelines | |
dc.subject.en | Haplotype reconstruction | |
dc.title.en | Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection | |
dc.type | Document de travail - Pré-publication | |
dc.type | Prepublication/Preprint | |
dc.identifier.doi | 10.5281/zenodo.4273791 | |
dc.subject.hal | Sciences du Vivant [q-bio] | |
dc.subject.hal | Sciences du Vivant [q-bio]/Biologie végétale | |
dc.subject.hal | Sciences du Vivant [q-bio]/Biologie végétale/Phytopathologie et phytopharmacie | |
hal.identifier | hal-03369187 | |
hal.version | 1 | |
hal.origin.link | https://hal.archives-ouvertes.fr//hal-03369187v1 | |
bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.date=2021-04-02&rft.au=TAMISIER,%20Lucie&HAEGEMAN,%20Annelies&FOUCART,%20Yoika&FOUILLIEN,%20Nicolas&AL%20RWAHNIH,%20Maher&rft.genre=preprint&unknown |
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