ReviewMicroorganisms2021
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses.
Review in Microorganisms, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 70 citations in OpenAlex.
- Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.PLoS pathogens · 2026Article
- High-Throughput Sequencing Reveals Regional Diversification of Cucurbit-Infecting Begomoviruses in Eastern Saudi Arabia.Viruses · 2026Article
- Virome metatranscriptomic profiling of birch pollen reveals a diverse viral community.Frontiers in plant science · 2026Article
- A Virome Scanning of Saffron (Viruses · 2025Article
- Article
- Virome analysis of field-collected chilli samples reveals diverse viruses.Virology journal · 2025Article
- MicroRNAs in Plant Genetic Regulation of Drought Tolerance and Their Function in Enhancing Stress Adaptation.Plants (Basel, Switzerland) · 2025Review
- Viroscope™: a universal solution for plant virus and viroid diagnostics using HTS and cloud-based analysis.Frontiers in microbiology · 2025Article
- High-throughput virome profiling reveals complex viral diversity, co-infection patterns, and novel viruses inFrontiers in plant science · 2025Article
- High-Throughput Sequencing for the Detection of Viruses in Grapevine: Performance Analysis and Best Practices.Viruses · 2024Article
- Article
- High-Throughput Sequencing Methods for the Detection of Two Strawberry Viruses in Post-Entry Quarantine.Viruses · 2024Article
- Simulated High Throughput Sequencing Datasets: A Crucial Tool for Validating Bioinformatic Pathogen Detection Pipelines.Biology · 2024Article
- Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding.Viruses · 2024Article
- Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran.Viruses · 2024Article
- AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data.Frontiers in genetics · 2024Article
- PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.BMC bioinformatics · 2023Article
- Article
- Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.Journal of virology · 2023Article
- Article
Corrections and comments
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Authors and funding
22 authors at 14 institutions in 10 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.