The development of high-throughput sequencing (HTS) technologies has revolutionized plant virology. One of the many application of HTS is the detection and diagnostics of plant viruses. The main advantage of HTS compared to other diagnostics methods is its unbiased nature, meaning that it is capable of detecting any virus present in the sample. Thus, it is particularly suitable for the discovery of new viruses. This chapter provides a step-by-step guide on how geminivirus diagnosis is performed using short-read HTS.
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