A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
MDPI
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/114849 |
| _version_ | 1855514754363162624 |
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| author | Kutnjak, D. Tamisier, Lucie Adams, I. Boonham, N. Candresse, T. Chiumenti, M. Jonghe, K. Kreuze, Jan F. Lefebvre, M. Silva, G. Malapi-Wight, M. Margaria, P. Mavrič Pleško, I. McGreig, S. Miozzi, L. Remenant, B. Reynard, J.S. Rollin, J. Rott, M. Schumpp, O. Massart, S. Haegeman, A. |
| author_browse | Adams, I. Boonham, N. Candresse, T. Chiumenti, M. Haegeman, A. Jonghe, K. Kreuze, Jan F. Kutnjak, D. Lefebvre, M. Malapi-Wight, M. Margaria, P. Massart, S. Mavrič Pleško, I. McGreig, S. Miozzi, L. Remenant, B. Reynard, J.S. Rollin, J. Rott, M. Schumpp, O. Silva, G. Tamisier, Lucie |
| author_facet | Kutnjak, D. Tamisier, Lucie Adams, I. Boonham, N. Candresse, T. Chiumenti, M. Jonghe, K. Kreuze, Jan F. Lefebvre, M. Silva, G. Malapi-Wight, M. Margaria, P. Mavrič Pleško, I. McGreig, S. Miozzi, L. Remenant, B. Reynard, J.S. Rollin, J. Rott, M. Schumpp, O. Massart, S. Haegeman, A. |
| author_sort | Kutnjak, D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects. |
| format | Journal Article |
| id | CGSpace114849 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1148492023-12-27T19:28:39Z A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses Kutnjak, D. Tamisier, Lucie Adams, I. Boonham, N. Candresse, T. Chiumenti, M. Jonghe, K. Kreuze, Jan F. Lefebvre, M. Silva, G. Malapi-Wight, M. Margaria, P. Mavrič Pleško, I. McGreig, S. Miozzi, L. Remenant, B. Reynard, J.S. Rollin, J. Rott, M. Schumpp, O. Massart, S. Haegeman, A. plant viruses bioinformatics detection genomes nucleic acids virology microbiology High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects. 2021-04-14 2021-09-02T05:00:49Z 2021-09-02T05:00:49Z Journal Article https://hdl.handle.net/10568/114849 en Open Access MDPI Kutnjak, D., Tamisier, L., Adams, I., Boonham, N., Candresse, T., Chiumenti, M., de Jonghe, K., Kreuze, J. F., Lefebvre, M., Silva, G., Malapi-Wight, M., Margaria, P., Mavrič Pleško, I., McGreig, S., Miozzi, L., Remenant, B., Reynard, J. S., Rollin, J., Rott, M., Schumpp, O., Massart, S., Haegeman, A. (2021). A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms. ISSN 2076-2607. 9(4). 841. 30 p. |
| spellingShingle | plant viruses bioinformatics detection genomes nucleic acids virology microbiology Kutnjak, D. Tamisier, Lucie Adams, I. Boonham, N. Candresse, T. Chiumenti, M. Jonghe, K. Kreuze, Jan F. Lefebvre, M. Silva, G. Malapi-Wight, M. Margaria, P. Mavrič Pleško, I. McGreig, S. Miozzi, L. Remenant, B. Reynard, J.S. Rollin, J. Rott, M. Schumpp, O. Massart, S. Haegeman, A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title | A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title_full | A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title_fullStr | A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title_full_unstemmed | A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title_short | A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses |
| title_sort | primer on the analysis of high throughput sequencing data for detection of plant viruses |
| topic | plant viruses bioinformatics detection genomes nucleic acids virology microbiology |
| url | https://hdl.handle.net/10568/114849 |
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