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Coronavirus Software

A Robust and Efficient Coronavirus Software Suite

A Robust and Efficient Coronavirus Software Suite

To support researchers with analysis and sharing of genomic data in relation to the severe acute respiratory syndrome coronavirus outbreak, Illumina has released the Illumina SARS-CoV-2 NGS Data Toolkit – a new suite of data analysis tools and functionality for scientists working with the virus.

These tools make it simpler for researchers to detect and identify the SARS-CoV-2 viral sequence in their samples, and contribute their findings to critical public databases.

Illumina SARS-Cov-2 NGS Data Toolkit
Detection & Identification Sharing & Collaboration
DRAGEN Metagenomocs New DRAGEN RNA Pathogen Detection App DRAGEN Metagenomocs SRA Import App
DRAGEN Metagenomocs New DRAGEN Metagenomics App DRAGEN Metagenomocs New GISAID Submission App
The Illumina SARS-CoV-2 NGS Data Toolkit is available on BaseSpace Sequence Hub. The DRAGEN RNA Pathogen Detection and DRAGEN Metagenomics Pipelines will also be made available on the DRAGEN Server in the coming weeks.

About the Illumina SARS-CoV-2 NGS Data Toolkit

This coronavirus detection and identification software is available to the community free of charge on BaseSpace Sequence Hub. The toolkit is comprised of several tools built on the Illumina DRAGEN Bio-IT Platform, and data submission apps on BaseSpace Sequence Hub, which empower researchers to seamlessly submit their findings to public databases.

Comprehensive Workflow Management and Sample Tracking Through BaseSpace Clarity LIMS

Clarity LIMS Respiratory Virus Panel Workflow

Accelerate Comprehensive Workflow Management and Sample Tracking Through BaseSpace Clarity LIMS

Two new workflows are available for BaseSpace Clarity LIMS:

  1. CDC COVID-19 RT-PCR workflow based on CDC recommendations
  2. Respiratory Virus Panel workflow using Nextera Flex for Enrichment library prep kit

These new workflows can help ensure samples are viable for analysis – allowing laboratories to quickly start processing coronavirus samples from sample accessioning and library prep to performing QC on sequencing runs.

Additional information about the Clarity LIMS COVID-19 tools can be found on our Software Blog.

Coronavirus Software for Clinical Applications

The Illumina SARS-CoV-2 NGS Data Toolkit is for research use only. For those seeking bioinformatics analysis and clinical reporting software, Illumina recommends the IDbyDNA Explify® Platform, now accessible on BaseSpace Sequence Hub. To request access, please contact IDbyDNA.

Learn More
Coronavirus Software for Clinical Applications
About the Illumina SARS-CoV-2 NGS Data Toolkit

Researchers can process samples using Clarity LIMS. Once sequencing is complete, researchers can automatically stream their data into BaseSpace Sequence Hub using the new toolkit.

Powering End-to-End Solutions for
SARS-CoV-2 Detection

Illumina is making it simpler to detect and identify SARS-CoV-2 using NGS with comprehensive, integrated workflows.

Compatible with the Illumina respiratory virus target enrichment workflow, the new toolkit empowers researchers to securely stream data directly off of our full portfolio of sequencers into BaseSpace Sequence Hub for rapid, comprehensive analysis using the DRAGEN RNA Pathogen Detection App. Once analysis is complete, researchers can submit their data to the Global Initiative on Sharing All Influenza Data (GISAID) directly from BaseSpace Sequence Hub.

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.

DRAGEN
                    Metagenomics Pipeline

DRAGEN Coronavirus Software Tools

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 for infectious disease detection as well as a DRAGEN Metagenomics Pipeline for outbreak surveillance. The DRAGEN coronavirus tools can be accessed on BaseSpace Sequence Hub, and will be made available on the DRAGEN Server starting May 2020. Additional information about use of the DRAGEN Platform for coronavirus detection and identification can be found here.

DRAGEN RNA Pathogen Detection Pipeline for Infectious Disease Detection

An updated version of the DRAGEN RNA Pipeline is now available to accelerate detection of viral pathogens. The new pipeline helps detect SARS-CoV-2 in any DRAGEN RNA-Seq Pipeline run, regardless of application. This pipeline includes:

  • Comprehensive detection, leveraging both coverage and k-mer based approaches to detect viral pathogens
  • Compatibility with the Illumina respiratory virus target enrichment workflow
  • Human and viral references using a combination of the human genome reference (hg38) with selected virus reference sequences
  • Integrated FASTA generation for upload to public databases, such as GISAID

The updated DRAGEN RNA Pathogen Detection App is now available on BaseSpace Sequence Hub, and will be available on the DRAGEN Server in the next few weeks. Additional details can be found here.

DRAGEN Metagenomics Pipeline for Outbreak Surveillance

This new pipeline helps drive rapid and simplified species-level detection in shotgun metagenomics samples. The pipeline is a metagenomics classification workflow able to detect and quantify SARS-CoV-2 sequences at high sensitivity and specificity while simultaneously providing readouts for other common viral and microbial pathogens.

The pipeline leverages an updated database which includes reads specific to coronavirus and delivers a breadth of outputs including Krona plots, organism detection, and QC reports. With the ability to analyze multiple different samples at once, the BaseSpace app enables researchers to look at clusters. Additional information can be found here.

See below for sample data generated by the DRAGEN Metagenomics App on BaseSpace Sequence Hub:

Krona Classification Chart
Organism Detection Chart
Powering the Heroes on the Front Lines to Address a Pandemic

Our sequencing solutions are being used to track transmission, conduct surveillance, and develop vaccines.

How We Help Fight COVID-19
Easy and Secure Sharing, Collaboration, and Submission to Public Databases

Easy and Secure Sharing, Collaboration, and Submission to Public Databases

BaseSpace Sequence Hub is designed to facilitate secure, audit-controlled collaboration among research groups. Data management and sharing capabilities, such as workgroups, allow you to share projects and runs securely with collaborators without requiring file downloads.

The new toolkit features several BaseSpace Sequence Hub apps for collaboration. The new GISAID Submission App accepts a collection of VCF or FASTA files, along with a metadata CSV for the same samples. The app performs data validation before submitting data to GISAID for further QA and processing.

Download BaseSpace Security and Privacy Info

How to Access the Illumina SARS-CoV-2 NGS Data Toolkit

The full Illumina SARS-CoV-2 NGS Data Toolkit is available on BaseSpace Sequence Hub. The updated DRAGEN COVID-19 tools will also be made available on the DRAGEN Server and will be made available to developers via the DRAGEN API.*

The Illumina SARS-CoV-2 NGS Data Toolkit on BaseSpace Sequence Hub

Researchers can start using the Illumina SARS-CoV-2 NGS Data Toolkit today on BaseSpace Sequence Hub, free of charge until Oct. 31, 2020. Researchers can stream data directly from their instruments into BaseSpace’s secure cloud environment for push-button usage of the entire toolkit.

Learn More About BaseSpace
Coronavirus Tools on the DRAGEN Server

The DRAGEN RNA Pathogen Detection and DRAGEN Metagenomics Pipeline will be available for download in May 2020 on the DRAGEN Server using the regular channels for installing new versions. Additional information can be found in the user guide.

DRAGEN Coronavirus Tools for Developers

Illumina will begin offering early access to its new DRAGEN API starting May 2020. The DRAGEN API is intended for large-scale research centers looking to automate analysis in the cloud. The API is built on top of Amazon Web Services. It allows users to call a simple API endpoint to stream, process, and deliver coronavirus sample data to and from their own AWS S3 bucket.

To request early access to the new DRAGEN coronavirus tools through the DRAGEN API, please complete the form below.

To request access to the DRAGEN API, please complete the form below.
The Illumina Community

Additional Software Tools

Target Enrichment Pipeline

The DRAGEN Enrichment Pipeline can also be leveraged for detection and identification of SARS-CoV-2. The pipeline is available on BaseSpace Sequence Hub for a low per-sample cost, and can be accessed on the DRAGEN Server.

Learn More

*The BaseSpace Sequence Hub SARS-CoV-2 NGS Data Toolkit is free of charge for 6 months, expiring October 31, 2020. Illumina is also providing a free 1-year trial of Clarity LIMS for COVID-19 researchers.