title: Targeted virus detection in next-generation sequencing data using an automated e-probe based approach.
abstract: The use of next-generation sequencing for plant virus detection is rapidly expanding, necessitating the development of bioinformatic pipelines to support analysis of these large datasets. Pipelines need to be easy implementable to mitigate potential insufficient computational infrastructure and/or skills. In this study user-friendly software was developed for the targeted detection of plant viruses based on e-probes. It can be used for both custom e-probe design, as well as screening preloaded probes against raw NGS data for virus detection. The pipeline was compared to de novo assembly-based virus detection in grapevine and produced comparable results, requiring less time and computational resources. The software, named Truffle, is available for the design and screening of e-probes tailored for user-specific virus species and data, along with preloaded probe-sets for grapevine virus detection.
authors.affiliation: Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: visserm@arc.agric.za.
authors.forename: Marike
authors.initials: M
authors.lastname: Visser
authors.affiliation: Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: jtb@sun.ac.za.
authors.forename: Johan T
authors.initials: JT
authors.lastname: Burger
authors.affiliation: Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa; Department of Genetics, Stellenbosch University, Stellenbosch, South Africa. Electronic address: hjmaree@sun.ac.za.
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Maree
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015342:DNA Probes; D066264:Datasets as Topic; D014644:Genetic Variation; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D010935:Plant Diseases / Q000821:virology; D010942:Plant Viruses / Q000235:genetics; D012984:Software; D014780:Viruses / Q000235:genetics*
chemical_list: D015342:DNA Probes
keywords: Bioinformatics; Grapevine; Grapevine leafroll disease; High-throughput sequencing; Virus diagnostics