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Development of a virus detection and discovery pipeline using next generation sequencing
Thien Ho1, Ioannis E Tzanetakis1
1Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA.
Virology
|December 3, 2014
Summary
A new bioinformatics tool, VirFind, streamlines virus discovery using next-generation sequencing (NGS). This pipeline aids plant virology by enabling efficient virus detection and identification of novel viral sequences.
Area of Science:
- Plant virology
- Bioinformatics
- Next-generation sequencing (NGS) technologies
Background:
- Next-generation sequencing (NGS) has significantly advanced virus discovery.
- A comprehensive bioinformatics pipeline for virus detection and discovery is lacking for the plant virology community.
Purpose of the Study:
- To develop a vertical pipeline for virus detection and discovery from sample preparation to data analysis.
- To construct VirFind, a bioinformatics tool for efficient virus detection and discovery in plants and insects.
Main Methods:
- Developed a degenerate oligonucleotide primed RT-PCR method with multiple barcodes for NGS.
- Constructed VirFind, a bioinformatics tool for mapping host reads, taxonomic classification, and conserved domain searches.
- Processed over 30 samples using the developed pipeline.
Main Results:
- Successfully detected all known viruses in the processed samples.
- Extended genomic sequences of existing viruses and discovered several novel viruses.
- VirFind demonstrated potential as a universal virus detection and discovery tool across plant and insect datasets.
Conclusions:
- The developed pipeline and VirFind tool provide a comprehensive solution for virus detection and discovery.
- VirFind facilitates the identification of known, extended, and novel viral sequences.
- The tool's successful application in external tests highlights its versatility and potential impact on virology research.
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