Over the past years next generation sequencing technology has opened doors to analyse and/or discover viral populations in any organism. A substantial number of studies has been performed which employ next generation sequencing techniques to either analyse known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Also BaseClear has already considerable experience in this field, as is demonstrated by article published in ‘Frontiers of microbiology‘. In this article bioinformatics approaches for viral metagenomics in plants using short RNAs are described. In addition BaseClear, in collaboration with BKD (Bloembollenkeuringsdienst), has developed the Virus diagnostics 2.0 browser.