Section: Genomics
Topic: Genetics/Genomics, Plant biology, Microbiology

Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

10.24072/pcjournal.62 - Peer Community Journal, Volume 1 (2021), article no. e53.

Get full text PDF Peer reviewed and recommended by PCI

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).

Published online:
DOI: 10.24072/pcjournal.62
Type: Software tool
Tamisier, Lucie 1; Haegeman, Annelies 2; Foucart, Yoika 2; Fouillien, Nicolas 1; Al Rwahnih, Maher 3; Buzkan, Nihal 4; Candresse, Thierry 5; Chiumenti, Michela 6; De Jonghe, Kris 2; Lefebvre, Marie 5; Margaria, Paolo 7; Reynard, Jean Sébastien 8; Stevens, Kristian 9, 3; Kutnjak, Denis 10; Massart, Sébastien 1

1 Université de Liège, Terra-Gembloux Agro-Bio Tech, Plant Pathology Laboratory, Passage des Déportés, 2, 5030 Gembloux, Belgium
2 Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
3 Department of Plant Pathology, University of California, Davis, California 95616, USA
4 Department of Plant Protection, Faculty of Agriculture, University of Sütçü Imam, Kahramanmaras 46060, Turkey
5 Univ. Bordeaux, INRAE, UMR BFP, CS20032, 33882 Villenave d’Ornon cedex, France
6 Institute for Sustainable Plant Protection, CNR, Via Amendola 122/D, Bari 70126, Italy
7 Leibniz Institute - DSMZ, German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
8 Virology, Agroscope, Nyon, Switzerland
9 Department of Evolution and Ecology, University of California, Davis, California 95616, USA
10 Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
     author = {Tamisier, Lucie and Haegeman, Annelies and Foucart, Yoika and Fouillien, Nicolas and  Al Rwahnih, Maher and Buzkan, Nihal and Candresse, Thierry and Chiumenti, Michela and De Jonghe, Kris and Lefebvre, Marie and Margaria, Paolo and Reynard, Jean S\'ebastien and Stevens, Kristian and Kutnjak, Denis and Massart, S\'ebastien},
     title = {Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection},
     journal = {Peer Community Journal},
     eid = {e53},
     publisher = {Peer Community In},
     volume = {1},
     year = {2021},
     doi = {10.24072/pcjournal.62},
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AU  - Tamisier, Lucie
AU  - Haegeman, Annelies
AU  - Foucart, Yoika
AU  - Fouillien, Nicolas
AU  -  Al Rwahnih, Maher
AU  - Buzkan, Nihal
AU  - Candresse, Thierry
AU  - Chiumenti, Michela
AU  - De Jonghe, Kris
AU  - Lefebvre, Marie
AU  - Margaria, Paolo
AU  - Reynard, Jean Sébastien
AU  - Stevens, Kristian
AU  - Kutnjak, Denis
AU  - Massart, Sébastien
TI  - Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection
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PY  - 2021
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DO  - 10.24072/pcjournal.62
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%A Haegeman, Annelies
%A Foucart, Yoika
%A Fouillien, Nicolas
%A  Al Rwahnih, Maher
%A Buzkan, Nihal
%A Candresse, Thierry
%A Chiumenti, Michela
%A De Jonghe, Kris
%A Lefebvre, Marie
%A Margaria, Paolo
%A Reynard, Jean Sébastien
%A Stevens, Kristian
%A Kutnjak, Denis
%A Massart, Sébastien
%T Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection
%J Peer Community Journal
%D 2021
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%R 10.24072/pcjournal.62
%F 10_24072_pcjournal_62
Tamisier, Lucie; Haegeman, Annelies; Foucart, Yoika; Fouillien, Nicolas;  Al Rwahnih, Maher; Buzkan, Nihal; Candresse, Thierry; Chiumenti, Michela; De Jonghe, Kris; Lefebvre, Marie; Margaria, Paolo; Reynard, Jean Sébastien; Stevens, Kristian; Kutnjak, Denis; Massart, Sébastien. Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Peer Community Journal, Volume 1 (2021), article  no. e53. doi : 10.24072/pcjournal.62.

Peer reviewed and recommended by PCI : 10.24072/pci.genomics.100007

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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