After the sequencing run ends, the generated fastq files can be imported into the JSI virSEAK software tool. virSEAK will automatically create a consensus sequence and alignment to the reference genome. It will show the claid where the sample belongs to and generate a .csv report of the mutations. Data will be compared to global databases (like GISAID) and you will be shown the subtype frequencies and distribution per country, as well as the evolution of the strain.
Results can be uploaded to the GISAID database with a single mouse-click in order to share the results with the global Covid community. It also provides an exportable consensus sequence for a more detailed analysis in local healthcare systems. For instance when investigating patient clusters or re-infections.