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.

On-the-fly analysis of viral communities in plants and animals

This browser allows on-the-fly analysis of viral communities in both plants and animals. For animals (such as fish) we can either use an approach were a host genome is available or an approach were no host genome is available. If the host genome is available, we can do a reference alignment against available host genome, after which the unaligned reads are assembled into contigs. Next the contigs are blast against available databases.

Virus discovery in plants

For virus discovery in plants we either sequence total RNA or only small-RNA. Next we can do a reference alignment against virus- or NCBI database, or alternatively we can do a De novo assembly and a BLAST of the generated contigs. The Virus diagnostics 2.0 browser allows an interactive visualization of the results in an online web portal. Access to the webportal is available upon request.

Meet Walter Pirovano!

Walter Pirovano (PhD) is the Director of the Bioinformatics department and a member of the BaseClear Management Team. He supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.

Contact Walter

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