A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
MALAPI-WIGHT, Martha
United States Department of Agriculture - Animal and Plant Health Inspection Service
United States Department of Agriculture - Animal and Plant Health Inspection Service
MARGARIA, Paolo
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
< Leer menos
Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures [DSMZ]
Idioma
en
Article de revue
Este ítem está publicado en
Microorganisms. 2021-04-14, vol. 9, n° 4, p. 841
MDPI
Resumen en inglés
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 ...Leer más >
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< Leer menos
Palabras clave
Pathologie Végétale
Virologie végétale
Santé des plantes
Palabras clave en inglés
plant virus
high-throughput sequencing
bioinformatics
detection
discovery
Orígen
Importado de HalCentros de investigación