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.
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.
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:
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.
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
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
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
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.*
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
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.
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.
The BaseSpace Sequence Hub is powered by Amazon Web Services and enables you to manage and analyze your data easily with a curated set of analysis apps. iCredits are a new form of currency used to purchase Illumina genomic data storage and analysis options.
The Illumina DRAGEN Bio-IT Platform provides accurate, ultra-rapid secondary analysis of sequencing data.
The NextSeq 1000 and NextSeq 2000 Systems support 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.
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.