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References from Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Local targets link to admitted publications; unresolved targets remain external evidence.
Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data
10.1099/jgv.0.001210 · 2019 · External reference
Next-generation sequencing technologies in diagnostic virology
10.1016/j.jcv.2013.03.003 · 2013 · External reference
Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline
10.1111/aab.12345 · 2017 · External reference
Methods in virus diagnostics: From ELISA to next generation sequencing
10.1016/j.virusres.2013.12.007 · 2014 · External reference
A new emaravirus discovered in Pistacia from Turkey
10.1016/j.virusres.2019.01.012 · 2019 · External reference
Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets
10.1111/1755-0998.13309 · 2021 · External reference
RNA virus mutations and fitness for survival
10.1146/annurev.micro.51.1.151 · 1997 · External reference
Virus Evolution: Insights from an Experimental Approach
10.1146/annurev.ecolsys.38.091206.095637 · 2007 · External reference
Evaluation of haplotype callers for next-generation sequencing of viruses
10.1016/j.meegid.2020.104277 · 2020 · External reference
A comparison of tools for the simulation of genomic next-generation sequencing data
10.1038/nrg.2016.57 · 2016 · External reference
An Analysis of the Durability of Resistance to Plant Viruses
10.1094/phyto.2003.93.8.941 · 2003 · External reference
Development of a virus detection and discovery pipeline using next generation sequencing
10.1016/j.virol.2014.09.019 · 2014 · External reference
Sequence characteristics of potato virus Y recombinants
10.1099/vir.0.014142-0 · 2009 · External reference
ART: a next-generation sequencing read simulator
10.1093/bioinformatics/btr708 · 2012 · External reference
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice
10.3389/fpls.2017.01770 · 2017 · External reference
IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
10.1093/gigascience/giaa111 · 2020 · External reference
Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences
10.1371/journal.pone.0216713 · 2019 · External reference
The VirAnnot Pipeline: A Resource for Automated Viral Diversity Estimation and Operational Taxonomy Units Assignation for Virome Sequencing Data
10.1094/pbiomes-07-19-0037-a · 2019 · External reference
Next-Generation Sequencing for Infectious Disease Diagnosis and Management
10.1016/j.jmoldx.2015.07.004 · 2015 · External reference
The Evolution and Genetics of Virus Host Shifts
10.1371/journal.ppat.1004395 · 2014 · External reference
The EMBL-EBI search and sequence analysis tools APIs in 2019
10.1093/nar/gkz268 · 2019 · External reference
Application of HTS for Routine Plant Virus Diagnostics: State of the Art and Challenges
10.3389/fpls.2018.01082 · 2018 · External reference
Analysing recombination in nucleotide sequences
10.1111/j.1755-0998.2011.03026.x · 2011 · External reference
Virus Detection by High-Throughput Sequencing of Small RNAs: Large-Scale Performance Testing of Sequence Analysis Strategies
10.1094/phyto-02-18-0067-r · 2019 · External reference
Current impact and future directions of high throughput sequencing in plant virus diagnostics
10.1016/j.virusres.2014.03.029 · 2014 · External reference
Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses
10.1128/jvi.01998-18 · 2019 · External reference
High-throughput sequencing technologies for plant pest diagnosis: challenges and opportunities
10.1111/epp.12472 · 2018 · External reference
Grapevine red blotch virus: Absence in Swiss Vineyards and Analysis of Potential Detrimental Effect on Viticultural Performance
10.1094/pdis-07-17-1069-re · 2018 · External reference
Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids
10.1094/pdis-03-17-0306-re · 2017 · External reference
Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes
10.1093/bib/bbs081 · 2014 · External reference
A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales
10.3390/v10080406 · 2018 · External reference
Targeted virus detection in next-generation sequencing data using an automated e-probe based approach
10.1016/j.virol.2016.05.008 · 2016 · External reference
Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms
10.1146/annurev-phyto-080614-120030 · 2015 · External reference
VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs
10.1016/j.virol.2016.10.017 · 2017 · External reference
