Main features

•  Tailored quality assessment and variant calling with intuitive visual and quality indicators 
•  Accurate detection of areas with low coverage and warnings for the user 
•  Integrated access to public databases and community-level data, including the GISAID EpiCOV™ database for worldwide variant frequencies 
•  FASTA files generation per-sample or per-run for additional downstream applications
•  Streamlined analysis and shorter turnaround time for results

SOPHiA’s protocol and pipeline are tested and optimized for fast and accurate analyses of SARS-CoV-2 whole genome providing

•  Yes/No reporting of viral presence
•  Automatic clade detection  
•  Confident variant calling

Paragon CleanPlex® SARS-CoV-2 powered by SOPHiA

Paragon CleanPlex® SARS-CoV-2 powered by SOPHiA offers a comprehensive solution for SARS-CoV-2 research and surveillance. Covering the whole genome of SARS-CoV-2, this solution provides high quality viral sequences and variant calling, enabling downstream analyses of the virus for tracking, therapeutic and prevention research to gain insights in disease susceptibility and severity.

For a demonstration of the SOPHiA Platform at work or for additional information, get in touch with an expert at info(at)


Turn Your Sequencing Lab Into a COVID-19 Research and Surveillance Powerhouse Q&A

SOPHiA GENETICS and Paragon Genomics came together recently to discuss their combined efforts in the fight against COVID-19.

> Re-watch the webinar on Youtube

Q&A Session

Q: What are some of the applications of sequencing the SARS-CoV-2 genome? 
A: The most immediate applications include monitoring the pandemic spreading through time and space – between countries or even within hospitals - and tracking the evolution of the viral genome for the development of treatments and/or vaccines. All these applications require high quality genome sequences.

Temporal resolution of the pandemic
Spatial (geographical) resolution of the pandemic
Viral genome diversity/evolution

Major applications of SARS-CoV-2 genomic analyses include temporal resolution, spatial (geographical) resolution, and viral genome diversity/evolution. Source: Nextstrain (
Q: How long is the total turn-around time?  
A: Our pipeline has been optimized with uploads as fast as only a few minutes – the result is a streamlined workflow of about 24 hours.
Q: Does this solution allow for assigning clades to the virus?  
A: Yes, it is possible to assign clades with data from the GISAID EpiCovTM, the largest database for SARS-CoV-2 used to retrieve allele frequencies. With SOPHiA Platform, the user can easily import metadata (e.g. date and place, sample type, qPCR results, etc.) relevant for your projects. For further downstream analyses, high-quality FASTA files are available for each sample.  
Q: Are there any further applications to be developed?
A: SOPHiA offers a multimodal approach for COVID-19, starting with the viral genome analysis and whole exome analysis of the host response. Coming soon, SOPHiA Radiomics for COVID-19 will enable the automatic radiomic feature extraction from full lung CTs .... stay tuned for more!  


Research Use Only, Not for Diagnosis
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