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Illumina releases software toolkit to support efforts to combat COVID-19

Illumina has announced the Illumina SARS-CoV-2 Data Toolkit, a new suite of data analysis tools and workflow functionality for researchers working with the virus using next-generation sequencing (NGS). 

The toolkit makes it easier for researchers to detect and identify the SARS-CoV-2 viral sequence in their samples and contribute their findings to critical public databases. Illumina is making the toolkit available at no cost to the global research community in support of efforts to combat the pandemic.

The toolkit integrates with Illumina’s worldwide installed base of 15,000 sequencing systems and is designed to help the global research community and public health officials track the path of the epidemic, understand transmission routes, determine the rate of viral evolution, and understand if the virus is changing in ways that impact therapeutic effectiveness. This connectivity across Illumina’s global technology platform allows researchers and public health officials to share information like never before.

‘NGS is on the front lines in the fight against COVID-19 and Illumina is proud to provide technology and support to track transmission, conduct surveillance, develop therapies and vaccines, and ensure long-term global safety and security,’ said senior vice president and chief medical officer, Dr Phil Febbo. ‘By design, these tools are applicable beyond COVID-19 to begin to build global capabilities for proactive surveillance of future outbreaks.’

The Illumina SARS-CoV-2 NGS Data Toolkit is releasing new and updated DRAGEN functionality, leveraging the speed and accuracy of DRAGEN to accelerate infectious disease surveillance and outbreak response. The toolkit includes a new DRAGEN RNA Pathogen Detection Pipeline to enable detection of infectious diseases, as well as a DRAGEN Metagenomics Pipeline for outbreak surveillance, an SRA Import App, as well as a GISAID Sharing App.

Compatible with many Illumina workflows, including the respiratory virus target enrichment workflow, the new toolkit empowers researchers to securely stream data directly off of Illumina’s full portfolio of sequencers into BaseSpace Sequence Hub for rapid, comprehensive analysis using the DRAGEN RNA Pathogen Detection App. Once the analysis is complete, researchers can submit their data to public databases directly from BaseSpace Sequence Hub. Illumina is offering the new toolkit to the community on BaseSpace Sequence Hub, free of charge, until October 2020.

For researchers looking to enhance their lab efficiency, Clarity LIMS can be used to track and monitor COVID-19 samples, delivering a comprehensive end-to-end solution. Illumina is offering a free, 1-year license to any researcher using Clarity LIMS for COVID-19 testing. To simplify end-to-end COVID-19 sample tracking and workflow management through BaseSpace, two new workflows for RT-PCR and NGS have been added to Clarity LIMS.

The Illumina SARS-CoV-2 Data Toolkit is for research use only. For those seeking bioinformatics analysis and clinical reporting software, Illumina recommends the IDbyDNA’s Explify Platform, now available on BaseSpace Sequence Hub.

This software toolkit is for research use only and is not for use in diagnostic procedures.


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