Overview
DRAGEN secondary analysis is a powerful bioinformatics software suite that enables labs of all sizes to do more with their genomic data.
Key features
Analyze NGS data from any Illumina sequencing system with on-premises or cloud deployment options
Fully process a 40× whole human genome in, calling a wide range of variants (SNV, indel, CNV, SV, mosaic variants, star alleles, etc.) in 34 mins vs 8 hours with a traditional open source solution calling fewer variant types 1
Reduce FASTQ file sizes up to 5× with DRAGEN Original Read Archive (ORA)
Drive unprecedented accuracy with multigenome mapping with pangenome reference and machine learning
Highly scalable DRAGEN analysis tackles lengthy compute times and massive data sets without compromising accuracy or requiring large investments in bioinformatics infrastructure. Reconfigurable field-programmable gate array technology (FPGA) provides hardware-accelerated implementations of a variety of analysis algorithms.
DRAGEN apps and pipelines are available in a secure, compliant cloud environment through Illumina Connected Analytics and BaseSpace Sequence Hub . Select pipelines are also available via on-premises server and onboard the NovaSeq X Series, NextSeq 1000 and NextSeq 2000 Systems, and the MiSeq i100 Series.
Seamlessly integrate DRAGEN analysis pipelines with somatic oncology variant interpretation using Connected Insights on-premise via DRAGEN server.
DRAGEN v4.4 is now available on-premises and on cloud
Over a 30% improvement in structural variant calling accuracy on benchmark samples*
New architecture for multiomic workflows, optimized for Illumina multiomic assays such as Illumina Single Cell 3' RNA prep and Illumina Protein Prep
Introducing two out-of-the-box oncology analysis applications, Heme WGS and Solid WGS tumor/normal
Support for new AWS F2 instances, enabling faster DRAGEN analysis in the cloud
*HG002 benchmark sample used, with both NIST T2TQ100, Compared against HG002 NIST T2T Q100 v1.1_v0.019 (hg38) with Truvari v.4.2.2, and CMRG, – Compared against HG002 CMRG v1.0 (hg38) with Truvari v.4.2.2, benchmarks.
DRAGEN v4.3 is now available on NovaSeqX
Reduction in FP and FN with DRAGEN v4.3, including features such as multigenome mapper and pangenome reference
5x reduction in runtime with faster BCL convert
Supports up to 12 workflow / genome pairs on a single flow cell, with up to 32 unique configurations per workflow / genome pair
Execute mapping and alignment directly on instrument using DRAGEN and send the FASTQ/ORA and BAM/CRAM directly to BaseSpace Sequence Hub
DRAGEN is now available on the MiSeq i100 Series
Rapid results with comprehensive secondary analysis generated in two hours or less †
Highly efficient workflow with a single user touchpoint to VCF and/or html report and no intermediate file transfers
Exceptionally easy with an intuitive interface for non-expert users
† When run according to sample recommendations
Applications
DRAGEN secondary analysis applications provide comprehensive coverage for many experiment types in a single platform, including whole-genome sequencing, exome sequencing, single-cell RNA-Seq, and methylation analysis.
Software solutions for NGS analysis
Clarity LIMS
Efficient sample tracking and workflow management for genomics labs.
BaseSpace Sequence Hub
Streamlined cloud-based run setup and monitoring.
Local Run Manager
This software provides a user-friendly integrated solution for creating sequencing runs, monitoring run status, and analyzing data.
DRAGEN secondary analysis Accurate, comprehensive, and efficient analysis of NGS data.
Illumina Connected Analytics
Operationalize informatics and drive scientific insights with Illumina Connected Analytics. Contact us for information on pricing, subscriptions, and more.
BaseSpace Apps
BaseSpace Sequence Hub offers a wide variety of NGS data analysis apps for common Illumina sequencing methods.
Emedgene
Emedgene streamlines tertiary analysis workflows for rare disease genomics and other germline research applications.
Illumina Connected Insights
Illumina Connected Insights streamlines tertiary analysis workflows for oncology clinical research and other somatic research applications.
Correlation Engine
An interactive omics knowledge base and data search engine that puts private data into biological context with highly curated public omics data.
Illumina Connected Multiomics
A powerful cloud-based multiomic analysis and interpretation software, enabling sample-to-answer workflows with interactive visualizations, infrastructure scalability, and secure data management.
Related applications and methods
Whole-genome sequencing
Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.
Exome sequencing
Whole-exome sequencing is used to investigate protein-coding regions of the genome to uncover genetic influences on disease and population health.
RNA sequencing
RNA-Seq uses next-generation sequencing to analyze expression across the transcriptome, enabling scientists to detect known or novel features and quantify RNA.
Proteomics
Explore the entire set of proteins in an organism, also known as the proteome, with next-generation sequencing.
Plans and pricing
DRAGEN secondary analysis requires purchase of a one-year license for the on-premises server. All license types are available in five levels with throughput ranging from 100,000 GB (level 1) to 2,000,000 GB (level 5).
A DRAGEN license and onboard hardware are included with purchase of an Illumina sequencing system. If deploying DRAGEN on the cloud via BaseSpace Sequence Hub or Illumina Connected Analytics , you will need to purchase an annual subscription as well as additional iCredits to store and analyze your data.
Flexibility of DRAGEN pipelines
DRAGEN analysis provides the flexibility to insert a variety of input files and produce a range of output documents. Users can customize their experience and use and produce their desired file format. The actual steps vary for each pipeline.
Multiplatform accessibility
DRAGEN analysis pipeline access options with features designed to fit the NGS analysis needs of every lab.
DRAGEN analysis on Illumina cloud platforms
DRAGEN analysis on Illumina Connected Analytics couples the accuracy and speed of DRAGEN secondary analysis with the ability to customize analysis pipelines to operationalize informatics on a secure platform.
DRAGEN analysis on BaseSpace Sequence Hub provides push-button analysis capabilities in an intuitive, easy-to-use interface with the secure compliance and data storage features of BaseSpace Sequence Hub.
See sample data sets for various methods in BaseSpace Sequence Hub, or test DRAGEN secondary analysis apps of interest and evaluate results interactively. Search on the term “dragen” from within the page to view data specific to DRAGEN analysis.
View sample data sets
Meet Illumina DRAGEN secondary analysis
DRAGEN offers accurate, comprehensive, and efficient secondary analysis of NGS data.
Pioneering feline genetics with NGS
Basepaws, a Zoetis company, leverages DRAGEN secondary analysis to develop direct-to-consumer DNA kits that provide cat owners with insights about their pets' health.
Kazusa DNA Research Institute: How DRAGEN reduces analysis time on complex plant genomes
Dr. Sachiko Isobe shares how DRAGEN secondary analysis completed analysis of large plant genomes in about 1/40th the time of conventional methods.
Australia’s Koala Conservation program uses whole-genome sequencing to save species
Researchers from the University of Sydney use DRAGEN analysis to power WGS of rare and endangered species to inform conservation plans.
GeneDx: Enabling operational growth with DRAGEN
Kyle Retterer, Chief Innovation Officer at GeneDx, details how his company seamlessly integrated the DRAGEN server into its existing on-premises solution to lower costs and reduce turnaround times.
Other Resources
Can genomics stop the world’s leading cause of death?
Two DRAGENs help Cardio-CARE slay one petabyte of data to better understand heart disease in Hamburg.
Children’s Hospital Colorado delivers precision medicine to kids
How an entire institution successfully integrated genomics into everyday care
Illumina DRAGEN Server v4
20051343
Includes Advance Exchange support for the first year. Requires purchase of annual DRAGEN license. View less
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DRAGEN Server Lvl 1 1 year License
20060397
Throughput of 100,000 Gb on DRAGEN Server View less
DRAGEN Server Lvl 2 1 year License
20060398
Throughput of 250,000 Gb on DRAGEN Server View less
DRAGEN Server Lvl 3 1 year License
20060399
Throughput of 500,000 Gb on DRAGEN Server View less
DRAGEN Server Lvl 4 1 year License
20060400
Througput of 1,000,000 Gb on DRAGEN Server View less
DRAGEN Server Lvl 5 1 year License
20060401
Throughput of 2,000,000 Gb on DRAGEN Server View less
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How does DRAGEN achieve high variant calling accuracy?
DRAGEN achieves high accuracy through various state of art technologies including multigenome reference and machine learning algorithms. For details, view the Accuracy improvements in germline small variant calling technical note.
How does DRAGEN software achieve rapid data analysis?
DRAGEN analysis uses highly reconfigurable field-programmable gate arrays (FPGA) to provide hardware-accelerated implementations of genome analysis algorithms. The algorithms are implemented as logic circuits, which provide almost instantaneous outputs. FPGAs can perform operations in parallel and are thus not node-dependent, as is the case for CPU-based systems.
Can I install DRAGEN analysis software on my own server?
No, DRAGEN analysis can only be run on the DRAGEN server. Users are also issued independent licenses that tie the usage of their licenses to specific servers.
How do BaseSpace Sequence Hub DRAGEN apps differ from DRAGEN server pipelines?
The BaseSpace Sequence Hub DRAGEN apps mimic the pipelines found on the on-site DRAGEN server and should produce the same results as the on-site pipelines (of the same software version as the app). However, some pipelines and software versions available on the on-site DRAGEN server may not be available as a BaseSpace DRAGEN app. Efforts are made to release on-site pipelines as BaseSpace DRAGEN apps, as needed.
Is DRAGEN analysis an onsite or hosted solution?
DRAGEN analysis is available onsite, hosted, or as a hybrid of both through secure data transfer between physical and cloud-based DRAGEN systems. The hybrid solution gives users the flexibility to scale up workflows in the cloud when higher analysis capacity is required.
Can DRAGEN analysis handle concurrent users?
The DRAGEN analysis system can only be used by one user at a time. The best way to handle multiple users is to use a job queueing tool that can accept jobs from users and queue them for processing by the DRAGEN software. The tool would call the DRAGEN software with one job at a time, and then notify the user when a job is completed. DRAGEN analysis works well with Slurm or LSF (Load Sharing Facility) schedulers to manage multiple users.
Does DRAGEN analysis process multiple samples in parallel?
For onsite and cloud analysis, DRAGEN processes one sample at a time using all available FPGA and CPU resources. Typically, the run times are so fast that a single DRAGEN server can easily keep up with a NovaSeq 6000 System run. For large-scale WGS processing with many NovaSeq 6000 Systems, you may need additional DRAGEN servers. You can also schedule many DRAGEN instances in parallel in the cloud, where each instance processes one sample.
Which instruments support DRAGEN onboard?
Currently DRAGEN on instrument is available with NextSeq 1000/2000 and NovaSeq X, and does not require additional license. Applications and functionality onboard is instrument specific and differs from what is available onboard. Please refer to the application table for more details.
Frequently purchased
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References
Illumina internal data on file, 2024. Run time calculated using DRAGEN v4.3 on DRAGEN server v4. Includes calling Full suite of callers for structural variants, repeat expansions, and targeted callers.
