Coronavirus Software

A Robust and Efficient Coronavirus Software Suite

Robust and Efficient Coronavirus Software Tools

To support researchers with analysis and sharing of genomic data in relation to the severe acute respiratory syndrome coronavirus outbreak, Illumina has released a suite of tools to help identify mutations, characterize novel strains, and examine the virus and the host responses associated with it.

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

See how our software tools help:

Viral detection and identification

Clinical applications

Host response studies

Workflow management

                    Metagenomics Pipeline

DRAGEN Coronavirus Software Tools

The Illumina SARS-CoV-2 NGS Data Toolkit leverages the speed and accuracy of DRAGEN to accelerate infectious disease surveillance and outbreak response. The toolkit includes a DRAGEN Metagenomics Pipeline for identifying novel infectious disease pathogens, a DRAGEN RNA Pathogen pipeline for detection of viral pathogens, and the DRAGEN Lineage app for detection of SARS-CoV-2 mutations for epidemiology. The DRAGEN coronavirus tools can be accessed on BaseSpace Sequence Hub. Additional information about coronavirus detection and surveillance with the DRAGEN Platform can be found in this software blog post.

DRAGEN RNA Pathogen Detection Pipeline for Detection and Surveillance of Viral Pathogens

An updated version of the DRAGEN RNA Pipeline is now available to accelerate detection of viral pathogens. This 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

Access the DRAGEN RNA Pathogen Detection Pipeline

DRAGEN Metagenomics Pipeline for Detection and Characterization of Novel Pathogens

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 samples at once, the BaseSpace app allows researchers to look at clusters.

Access the DRAGEN Metagenomics Pipeline

View sample data generated by this pipeline:

Krona Classification Chart
Organism Detection Chart

This app aligns reads to a SARS-CoV-2 reference genome and reports coverage of targeted regions. It performs:

  • K-mer based detection
  • Map/align, variant calling
  • Consensus sequence generation
  • Lineage/clade analysis using Pangolin and NextClade

Access the DRAGEN COVID Lineage App



A Robust and Efficient Coronavirus Software Suite

Coronavirus Software for Clinical Applications

For users looking to generate clinical reporting of SARS-CoV-2 detection to diagnose COVID-19 in symptomatic patients, the DRAGEN COVIDSeq Test Pipeline is used in conjunction with the Illumina COVIDSeq Test.

For users looking to generate clinical reports for shotgun metagenomics, respiratory virus oligo panel, and respiratory pathogen ID/AMR panel, IDbyDNA delivers simple, powerful bioinformatics software to turn the data generated by our sequencers into actionable insights. IDbyDNA’s proven, automated Explify platform analysis supports the detection of 35 respiratory viruses, including genomic characterization of SARS-CoV-2. Contact IDbyDNA Client Services at 833-397-5439 or to learn more.


Comprehensive Workflow Management and Sample Tracking Through BaseSpace Clarity LIMS

Correlation Engine for Host Response Studies

Illumina is delivering a free, collaborative environment to the COVID-19 research community to better understand critical factors that regulate the host response and help identify biomarkers for potential treatments.

How BaseSpace Correlation Engine can advance your research:

  • Putting it into context: Correlation Engine mines thousands of genomic studies, allowing researchers to integrate their data with the world’s genomic knowledge base to generate data-driven answers.
  • Accelerating research: Reduce time to discovery by leveraging Correlation Engine to query thousands of studies instantaneously and help validate hypotheses by making data-driven queries in real time
  • Staying current: Illumina has a dedicated team committed to updating Correlation Engine with curated COVID-19 data, and welcomes members of the research community to contribute their findings to help advance COVID-19 research.
  • Integration: Correlation Engine is an integrated extension of our full stack of transcriptomics products to help researchers seamlessly navigate from sample to answer.
  • Collaboration: When it comes to the fight against COVID-19, we’re all in this together. Correlation Engine allows researchers to contribute and share their data with the research community to advance our understanding of COVID-19 host response.

Learn More About Correlation Engine
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Coronavirus Sequencing Solutions

Explore NGS methods and find solutions to detect and characterize SARS-CoV-2 and/or other respiratory pathogens, track transmission, study co-infection, and investigate viral evolution.

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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 Illumina SARS-CoV-2 NGS Data Toolkit features several BaseSpace Sequence Hub apps for collaboration. The 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 through July 31, 2021. 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
DRAGEN Coronavirus Tools for Developers

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 fill out the form below.

Featured Products

BaseSpace Sequence Hub and iCredits

BaseSpace Sequence Hub, powered by Amazon Web Services, allows you to manage and analyze your data easily with a curated set of analysis apps. iCredits are the currency used to purchase Illumina genomic data storage and analysis options.

DRAGEN Bio-IT Platform

The Illumina DRAGEN Bio-IT Platform provides accurate, ultra-rapid secondary analysis of sequencing data.

NextSeq 2000 System and Reagents

The NextSeq 2000 System supports emerging and mid-throughput sequencing applications as well as a broad range of methods such as exome sequencing, target enrichment, single-cell profiling, transcriptome sequencing, and more.

To request access to the DRAGEN API, please complete the form below.
COVID-19 Host Risk and Response

Understanding host genetic differences and individual responses to the SARS-CoV-2 virus increases understanding of disease susceptibiliity and severity. Read more about the methods for host risk & immune response studies.

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The Illumina Community

Additional Coronavirus 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.

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* The BaseSpace Sequence Hub SARS-CoV-2 NGS Data Toolkit is free of charge through July 31, 2021. Illumina is also providing a free 1-year trial of Clarity LIMS for COVID-19 researchers.