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DRAGEN secondary analysis is a powerful bioinformatics software suite that enables labs of all sizes to do more with their genomic data.
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 NextSeq 1000 System, NextSeq 2000 System, and NovaSeq X System.
| Instruments | MiSeq System, iSeq 100 System, NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, MiniSeq System, NovaSeq X System, NovaSeq X Plus System |
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| Software format | On-premises, Cloud, Onboard |
| Technology | Sequencing |
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.
Efficient sample tracking and workflow management for genomics labs.
Streamlined cloud-based run setup and monitoring.
Intuitive on-instrument run setup and monitoring.
DRAGEN secondary analysis
Accurate, comprehensive, and efficient analysis of NGS data.
Operationalize informatics and drive scientific insights with Illumina Connected Analytics. Contact us for information on pricing, subscriptions, and more.
BaseSpace Sequence Hub offers NGS data analysis apps for common Illumina sequencing methods.
Emedgene streamlines tertiary analysis workflows for rare disease genomics and other germline research applications.
An interactive omics knowledge base that analyzes private omics data with highly curated public data to help researchers put their data into biological context.
Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.
Whole-exome sequencing is used to investigate protein-coding regions of the genome to uncover genetic influences on disease and population health.
RNA-Seq uses next-generation sequencing to analyze expression across the transcriptome, enabling scientists to detect known or novel features and quantify RNA.
| Application | On-premises server | Onboard Illumina sequencing systems | On Illumina cloud platforms | ||
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| NovaSeq X Series | NextSeq 1000/2000 Systems | BaseSpace Sequence Hub | Illumina Connected Analytics | ||
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| DRAGEN ORA compression | checkmark
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| DRAGEN FASTQC + MultiQC | checkmark
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| Whole genome | Germline + Somatic | Germline Somatic (tumor-only) | Germline only | Germline + Somatic | Germline + Somatic |
| Enrichment (including Exome) | Germline + Somatic | Germline Somatic (tumor-only) | Germline Somatic (tumor-only) | Germline + Somatic | Germline + Somatic |
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| RNA | checkmark
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| Single-Cell RNA | checkmark
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| Differential Expression | checkmark
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| NanoString GeoMx NGS (spatial transcriptomics) | checkmark
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| Methylation | checkmark
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| Metagenomics* | checkmark
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| COVID | COVIDSeq, COVID lineage | COVIDSeq (cloud only) | COVIDSeq, COVID lineage | ||
| TruSight Oncology 500 | ctDNA and Solid |
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| Single-cell ATAC-Seq | checkmark
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*Metagenomics applications enabled by Kmer classifier. More tools coming soon.
Core DRAGEN version varies across platforms. Speak to a local representative for more information.
| Pipeline | Description | Variant types detected | Metrics provided |
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| DRAGEN Demultiplexing | Performs rapid demultiplexing of NGS analysis | N/A | N/A |
| DRAGEN ORA Compression | Optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, while preserving data integrity. | N/A |
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| DRAGEN Map + Align | Can be run as a standalone or as part of DRAGEN’s suite of pipelines | N/A |
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| DRAGEN Germline | Provides end-to-end NGS analysis, including advanced error model calibration for increased accuracy, and repeat expansion detection and genotyping through Illumina Expansion Hunter. |
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| DRAGEN Somatic | Includes tumor-only and tumor–normal modes designed for detecting somatic variants in tumor samples. Both modes make no ploidy assumptions, enabling detection of low-frequency alleles. |
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| DRAGEN Enrichment | Combines DRAGEN’s germline and somatic callers into a pipeline designed specifically for analyzing enrichment samples. Includes a full suite of enrichment metrics and reporting. |
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| DRAGEN RNA | Performs transcriptome analysis starting with splice junction discovery and alignment, followed by rapid alignment, splice junction mapping, and quantification. (For differential expression, try the DRAGEN Differential Expression app on BaseSpace Sequence Hub). |
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| DRAGEN Single Cell RNA | Performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression. | N/A |
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| DRAGEN Joint Genotyping | Calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy. |
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| DRAGEN Methylation | Performs alignment and methyl calling. Calculates alignment and methylation metrics. | N/A |
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| DRAGEN Reference Builder | Accepts FASTA files, and builds the proprietary reference used by the DRAGEN apps. | N/A | N/A |
| DRAGEN TruSight Oncology 500 ctDNA Analysis Software | Offers secondary analysis support for TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3). |
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| DRAGEN Imputation | Enables scalable low-pass whole-genome sequencing analysis in an end-to-end user-friendly tool. | N/A | Impute ≤100 samples simultaneously 1.7x faster compared to original GLIMPSE code |
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.
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.
DRAGEN analysis pipeline access options with features designed to fit the NGS analysis needs of every lab.
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.
DRAGEN offers accurate, comprehensive, and efficient secondary analysis of NGS data.
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.
Dr. Sachiko Isobe shares how DRAGEN secondary analysis completed analysis of large plant genomes in about 1/40th the time of conventional methods.
Researchers from the University of Sydney use DRAGEN analysis to power WGS of rare and endangered species to inform conservation plans.
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.
Two DRAGENs help Cardio-CARE slay one petabyte of data to better understand heart disease in Hamburg.
Illumina DRAGEN Server v4
20051343
Includes Avance Exchange support for the first year. Requires purchase of annual DRAGEN license.
List Price:
Discounts:
DRAGEN Server Lvl 1 1 year License
20060397
Throughput of 100,000 Gb on DRAGEN Server
DRAGEN Server Lvl 2 1 year License
20060398
Throughput of 250,000 Gb on DRAGEN Server
DRAGEN Server Lvl 3 1 year License
20060399
Throughput of 500,000 Gb on DRAGEN Server
DRAGEN Server Lvl 4 1 year License
20060400
Througput of 1,000,000 Gb on DRAGEN Server
DRAGEN Server Lvl 5 1 year License
20060401
Throughput of 2,000,000 Gb on DRAGEN Server
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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.
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.
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.
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.
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.
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.
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.
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.
Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.
Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.
Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.
A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.
Manage runs, analyze, store, and share sequencing data in BaseSpace Sequence Hub. Find applications, subscription options, and documentation.
Operationalize informatics and drive scientific insights with Illumina Connected Analytics. Contact us for information on pricing, subscriptions, and more.
A highly customizable laboratory information management system that allows genomics labs to track samples and manage workflows efficiently and securely.
References
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