Over the past years next generation sequencing technology has opened doors to analyze and/or discover viral populations in any organism. A substantial number of studies has been performed which employ next generation sequencing techniques to either analyze known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Also BaseClear has already consinderable experience in this field, as is demonstrated by article published in 'Frontiers of microbiology' (click here to read the full article). In this article bioinformatics approaches for viral metagenomics in plants using short RNAs are discribed. In addtition BaseClear, in collaboration with BKD (Bloembollenkeuringsdienst), has developed the Virus diagnostics 2.0 browser.
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 availble. If the host genome is available, we can do a reference alignment against availble host genome, after which the unaligned reads are assembled into contigs. Next the contigs are blast against available databases.
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. The portal is accessible via https://virusdiagnostics.baseclear.com and supported for Firefox, Internet Explorer (version 9 and higher) and Chrome and is a safe repository for all your virus diagnostics projects. Customization of the webportal and interface is available upon request.
Walter is director of the bioinformatics department and supervises our team of excellent bioinformaticians with expertise in the field of next-gen analysis and (far) beyond.
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