DRAGEN v4.2 Updates | New features include:

Increased SNV and SV calling accuracy powered by an enhanced machine learning model and multigenome (graph).
Improvements in small CNV calling accuracy with joint SV/CNV calling.
Includes new targeted callers for carrier screening: HBA 1/2, CYP21A2, RHD/RHCE, and LPA.
Additional information and full list of features can be found in the release notes.

Illumina DRAGEN Secondary Analysis

The Illumina DRAGEN Secondary Analysis provides accurate, comprehensive, and efficient analysis of next-generation sequencing data. Read More...

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On-Premise Server

Illumina DRAGEN Server v4

20051343

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DRAGEN Server Lvl 1 1 year License

20060397

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DRAGEN Server Lvl 2 1 year License

20060398

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DRAGEN Server Lvl 3 1 year License

20060399

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DRAGEN Server Lvl 4 1 year License

20060400

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20060401

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Product Highlights

DRAGEN analysis offers accurate, comprehensive, and efficient secondary analysis of next-generation sequencing data:

Continuous Innovation: Graph reference genome and machine learning driving unprecedented accuracy²
Hardware Acceleration: Provides ultra-efficient workflow; can fully process a 34x whole human genome in ~30 minutes with DRAGEN server v4¹
Lossless Compression: Furthers ultra-efficient workflow by reducing FASTQ file sizes up to 5× with DRAGEN ORA (Original Read Archive)
Broad Menu of Applications: Analyzes next-generation sequencing (NGS) data from whole genomes, exomes, methylomes, and transcriptomes
Flexible Configurability: Available on platform of choice and scalable based on needs

view video about Illumina DRAGEN – Accurate, Comprehensive, Efficient Secondary Analysis — Play Video

View Data Sheet

DRAGEN analysis offerings

DRAGEN On-Premise Server

DRAGEN Onboard

DRAGEN on Illumina Managed Cloud Platforms

Key Benefits

Accurate results

99.83% accuracy score with the Precision FDA Truth Challenge V2 benchmark data.³

Comprehensive platform

Analyze whole genomes, exomes, methylomes, and transcriptomes with a single platform.

Efficient analysis

Process a 34x genome in ~ 30 minutes, with all supported callers². Reduce FASTQ file sizes up to 5× with DRAGEN ORA Compression.

DRAGEN secondary analysis achieving award-winning accuracy

DRAGEN analysis leads in accuracy for germline and somatic variant calling demonstrated in industry challenges from precisionFDA.

DRAGEN analysis enables labs of all sizes and disciplines to do more with their genomic data. DRAGEN analysis uses highly reconfigurable field-programmable gate array technology (FPGA) to provide hardware-accelerated implementations of genomic analysis algorithms, such as BCL conversion, mapping, alignment, sorting, duplicate marking, and haplotype variant calling. DRAGEN ORA lossless genomic compression technology enables significant storage cost savings on FASTQ files. Fundamental features of DRAGEN analysis address common challenges in genomic analysis, such as lengthy compute times and massive volumes of data.

Without compromising accuracy, DRAGEN analysis delivers quickness, flexibility, and cost efficiency. The reprogrammable nature of DRAGEN analysis enables Illumina to develop custom algorithms and allows for improvements to accommodate future applications.

DRAGEN analysis

Key DRAGEN applications

	On-Premise Server	Onboard		On Illumina managed cloud platforms
		NovaSeq X Series	NextSeq 1000/2000	BaseSpace Sequence Hub	Illumina Connected Analytics
BCL Convert					Custom only
DRAGEN ORA compression
DRAGEN FASTQC + MultiQC
Whole genome	Germline + Somatic	Germline only Somatic coming soon	Germline only	Germline + Somatic	Germline + Somatic
Enrichment (including Exome)	Germline + Somatic	Germline + Somatic	Germline + Somatic	Germline + Somatic	Germline + Somatic
DNA Amplicon
RNA
Single-Cell RNA
Differential Expression
NanoString GeoMx NGS
RNA Amplicon					Coming soon
Methylation		Coming H2 2023
Metagenomics	^*
RNA Pathogen Detection
COVID	COVIDSeq, COVID lineage		Cloud only COVIDSeq	COVIDSeq, COVID lineage
TSO 500	ctDNA available Solid Coming Soon			Enabled in 3.10
Imputation
ScATAC-Seq
PGx Star Allele Caller		Coming soon
Illumina Complete Long Reads
DRAGEN Secondary Analysis for RPIP and UPIP panels	Beta			Beta	Beta

^*Metagenomics applications enabled by Kmer classifier, more tools coming soon

Core DRAGEN version varies across platforms, speak to a local representative for more information

Download table document

DRAGEN pipelines

Pipeline	Description	Variant Types Detected	Metrics Provided
DRAGEN Demultiplexing	Rapid demultiplexing of NGS analysis	N/A	N/A
DRAGEN Compression	DRAGEN ORA compression is optimized for high compression ratios of FASTQ files, as well as rapid compression and decompression, all while preserving data integrity.	N/A	Compression Ratio Run Time
DRAGEN Map + Align	The DRAGEN Map + Align can be run as a standalone or as part of DRAGEN’s suite of pipelines	N/A	Mapping metrics Duration Metrics Coverage Metrics
DRAGEN Germline	The DRAGEN Germline Pipeline provides end-to-end NGS analysis, including advanced error model calibration for increased accuracy, and repeat expansion detection and genotyping through Illumina Expansion Hunter.	SNV CNV SV Repeat Expansions	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Somatic	The DRAGEN Somatic Pipeline 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.	SNV CNV SV TMB MSI HLA	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Enrichment	The DRAGEN Enrichment Pipeline 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.	SNV CNV SV	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN RNA	The DRAGEN RNA Pipeline performs transcriptome analysis starting with splice junction discovery and alignment, followed by rapid alignment and splice junction mapping and quantification. For differential expression, Illumina recommends the DRAGEN Differential Expression app on BaseSpace Sequence Hub.	Gene fusion	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Single Cell RNA	The DRAGEN Single Cell RNA pipeline performs demultiplexing, cell-barcode and UMI error correction, sequence alignment, and quantification of gene expression.	N/A	Mapping Metrics Duration Metrics Coverage Metrics Callability Report Cell Metrics
DRAGEN Joint Genotyping	The DRAGEN Joint Genotyping/Population Pipeline calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy.	SNV CNV SV Repeat Expansions	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Methylation	The DRAGEN Methylation Pipeline performs alignment, methyl calling, and calculates alignment and methylation metrics.	N/A	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
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	Secondary analysis support for Illumina’s TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3)	SNV CNV DNA fusions MSI TMB	Mapping metrics Duration Metrics Coverage Metrics Variant Metrics Callability Report
DRAGEN Imputation	The DRAGEN Imputation pipeline is an end to end user friendly tool that enables scalable low pass whole genome sequencing analysis	N/A	Impute ≤100 samples simultaneously 1.7x faster compared to original GLIMPSE code

SARS-CoV-2 NGS Data Toolkit

Illumina is making it simpler for researchers to detect and identify SARS-CoV-2 and contribute their findings to the community with an integrated software toolkit, free of charge.

SARS-CoV-2 NGS Data Toolkit

DRAGEN analysis on Illumina Connected Analytics couples the accuracy and speed of the DRAGEN with the ability to customize analysis pipeline to operationalize informatics on a secure platform.

Learn about Illumina Connected Analytics

DRAGEN on BaseSpace Sequence Hub (BSSH) provides push button analysis capability in an intuitive, easy-to-use interface with compliance, and storage features of BaseSpace Sequence Hub and Amazon Web Services (AWS).

Learn about BaseSpace Sequence Hub

DRAGEN on BaseSpace Sequence Hub

DRAGEN on-premise server offers highly accurate secondary analysis in a fraction of time compared with a traditional CPU-based system.

Analyze and store data locally
Supports varying levels of command line interface
Replace up to 30 traditional compute instances
Fully process a 34× whole human genome in ~30 minutes². HG002 from PrecisionFDA truth challenge V2 run with DRAGEN analysis v4.0 on DRAGEN server v4, all callers
One unit supports two NovaSeq 6000 Systems running at full capacity

Read Data Sheet

DRAGEN On-Premise

DRAGEN onboard offers an accurate, comprehensive, and efficient secondary analysis solution for the NovaSeq X Series and NextSeq 1000/2000 Systems.

DRAGEN onboard NovaSeq X Series:

Flexibly runs multiple secondary analysis pipelines in parallel.
Performs up to four simultaneous applications per flow cell in a single run.
Brings up to 5x lossless data compression, and analysis with supported applications
Provides savings on analysis, which over five years can exceed the the price of the sequencer

Learn more about the NovaSeq X Series

DRAGEN onboard NextSeq 1000 and NextSeq 2000 Systems:

Provides access to select DRAGEN analysis informatics pipelines
Enables users to generate results in as little as two hours
Uses intuitive pipeline algorithms to reduce reliance on external informatics experts

Read Data Sheet

Pioneering feline genetics with NGS

Basepaws, a Zoetis company, leverages the Illumina DRAGEN secondary analysis to develop direct-to-consumer DNA kits that provide cat owners with insights about their pets' health.

Scaling to the cloud to support whole-genome sequencing

Kyle Retterer, MS, Chief Technology Officer of GeneDx, discusses use of DRAGEN in the cloud to scale computing and data storage. This evolution brought more data analysis speed, infrastructure security, cost efficiency, and simplicity to their data management.

Read Customer Spotlight

Bringing bioinformatics in-house reduces costs and turnaround time

Phosphorus uses DRAGEN secondary analysis to perform genomic data analysis onsite and at an accessible price point.

Can genomics stop cardiovascular disease?

Two DRAGEN servers help Cardio-CARE slay one petabyte of data to better understand heart disease in Hamburg.

DRAGEN analysis uses

DRAGEN analysis can be used in numerous fields in the biological sciences.

Genetic Diseases

Reduce time required for genomic analysis, with high accuracy and comprehensiveness

Oncology

Analyze tumor-only and tumor/normal samples with accuracy, comprehensiveness, and efficiency

Cell and Molecular Biology

Advance understanding of cellular mechanisms with rapid analysis pipelines for bulk and single cell samples

Population Genomics

Accurately and efficiently analyze sequenced genomes at scale. Accelerate re-analysis as computational tools improve over time

Infectious Disease

Detect and characterize infectious diseases with a comprehensive solution

Agrigenomics

Efficiently analyze animals and plants of varying genomic complexities with custom reference

References

Illumina data on file, 2022.
Illumina DRAGEN Secondary Analysis is the first single platform to achieve 99.83% accuracy based on PrecisionFDA v2 Truth Challenge Benchmark Data. Details here.
PrecisionFDA Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions. precision.fda.gov/challenges/10. Accessed November 3, 2020.

Frequently Purchased Together

Flexible and Customizable Pipelines

DRAGEN Germline Pipeline Steps

DRAGEN analysis provides the flexibility to insert a variety of input files and produce a range of output documents. This flexibility enables users to customize their experience and use and produce their desired file format.

This diagram shows steps in the DRAGEN Germline Pipeline as an example. The actual steps vary for each pipeline.

Product Literature

Basespace Sequencing Hub Apps Quick Guide

Brochure | PDF < 1 MB

Tumor exome sequencing with Illumina DNA Prep with Enrichment and the DRAGEN Platform

Application Note | PDF 1 MB

Integrating the Illumina DRAGEN Bio-IT Platform within your Infrastructure

Technical Note | PDF < 1 MB

DRAGEN Bio-IT Platform on BaseSpace Sequence Hub

Data Sheet | PDF 1 MB

DRAGEN Germline Pipeline Specification Sheet

Data Sheet | HTML

High-resolution, high-throughput spatial transcriptomics of complex tissues

Application Note | PDF 3 MB

High-plex spatial proteogenomics of FFPE tissue sections

Application Note | PDF 2 MB

Illumina Genomics Architecture enables PopGen studies with Illumina DNA PCR-Free Prep

Application Note | PDF 2 MB

Explore the transcriptome with single-cell resolution

Technical Note | PDF 1 MB

Technical Note | PDF | 3 versions

Technical Note | PDF | 2 versions

Data Sheet | PDF | 7 versions

Manuals and Support Information

DRAGEN Developer Resources Documentation

All DRAGEN Support

BaseSpace Sequence Hub

BaseSpace Sequence Hub

Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing (NGS) operations.

Illumina Connected Analytics

Illumina Connected Analytics

A secure genomic data platform to operationalize informatics and drive scientific insights.

Clarity LIMS

Clarity LIMS

Clarity LIMS is a laboratory information management system designed for genomics labs to track samples and manage workflows for an optimized and efficient lab.

Whole-Genome Sequencing (WGS)

Whole-genome sequencing delivers a comprehensive view, ideal for discovery applications. Newer genome sequencers perform WGS more rapidly than ever.

Learn More

Exome Sequencing

Whole-exome sequencing is used to investigate protein-coding regions of the genome to uncover genetic influences on disease and population health.

Learn More

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.

Learn More