Illumina DRAGEN Bio-IT Platform

Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform provides accurate, comprehensive, and efficient analysis of next generation sequencing data. Read More...

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On-Premise Server

Illumina DRAGEN Server v4



Illumina DRAGEN Server v3



DRAGEN Server Lvl 1 1 year License


DRAGEN Server Lvl 2 1 year License


DRAGEN Server Lvl 3 1 year License


DRAGEN Server Lvl 4 1 year License


DRAGEN Server Lvl 5 1 year License


Cloud: Amazon Web Services

DRAGEN AWS Lvl 1 1 year License


DRAGEN AWS Lvl 2 1 year License


DRAGEN AWS Lvl 3 1 year License


DRAGEN AWS Lvl 4 1 year License


DRAGEN AWS Lvl 5 1 year License


Cloud: Microsoft Azure

DRAGEN Azure Lvl 1 1 year License


DRAGEN Azure Lvl 2 1 year License


DRAGEN Azure Lvl 3 1 year License


DRAGEN Azure Lvl 4 1 year License


DRAGEN Azure Lvl 5 1 year License


Product Highlights

Accurate, comprehensive, and efficient secondary analysis of next-generation sequencing data. Illumina DRAGEN offers:
  • Continuous Innovation: Graph reference genome and machine learning driving unprecedented accuracy2
  • Hardware Acceleration: Provides ultra-efficient workflow; can fully process a 34x while 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
DRAGEN Offerings

DRAGEN on Illumina Connected Analytics

DRAGEN on BaseSpace Sequence Hub

DRAGEN On-Premise Server

DRAGEN on NextSeq 1000/2000

DRAGEN Multi-Cloud Bring Your Own License

DRAGEN on AWS Marketplace


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


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


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

DRAGEN Sets New Standards for Data Accuracy with Precision FDA Benchmark Data

The DRAGEN team has introduced powerful machine learning (ML) and improved graph genome mapping. These new advancements propel DRAGEN to lead accuracy across all read technologies in all benchmark regions and the MHC region. In this blog, we show the results collected in the PrecisionFDA Truth Challenge V2, compare the latest DRAGEN accuracy against the challenge submissions across all read technologies, and describe the methods used to reach high accuracy levels.

Read Blog

The DRAGEN Platform enables labs of all sizes and disciplines to do more with their genomic data. The DRAGEN Platform 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 the DRAGEN Platform address common challenges in genomic analysis, such as lengthy compute times and massive volumes of data.

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

Key DRAGEN Applications

  DRAGEN On-Premise Server NextSeq 1000/2000 BaseSpace Illumina Connected Analytics Multi-Cloud Bring Your Own License
        Pre-configured Build your own  
BCL Convert           Not recommended on FPGA
DRAGEN ORA compression            
DRAGEN FASTQC + MultiQC            
Whole genome Germline + Somatic Germline Germline + Somatic Germline + Somatic Germline + Somatic Germline + Somatic
Enrichment (including Exome) Germline + Somatic Germline + Somatic Germline + Somatic Germline + Somatic Germline + Somatic Germline + Somatic
DNA Amplicon            
Single-Cell RNA            
Differential Expression            
NanoString GeoMx NGS            
RNA Amplicon       Coming soon    
RNA Pathogen Detection            
COVID Lineage       Coming soon Coming soon  
TSO 500 ctDNA and Solid Coming soon for DRAGEN v3.10     ctDNA and Solid Coming soon for DRAGEN v3.10    
PGx Star Allele Caller            
Download table document
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.

Learn More
SARS-CoV-2 NGS Data Toolkit

DRAGEN on Illumina Connected Analytics (ICA) 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 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 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

The on-board DRAGEN offers an easy to use, accurate, and efficient secondary analysis solution.

  • Seamlessly integrates sequencing and analysis in run setup. Instead of sequencing stopping at BCL file generation, DRAGEN onboard enables FASTQ and VCF file generation as the sequencing run completes
  • Save time on file transfer and analysis run time
  • Access to a select menu of DRAGEN applications

Read Data Sheet

DRAGEN on AWS and Azure gives you access to DRAGEN software in a virtual image on your preferred cloud.

  • Utilizes the same software and command-line options as DRAGEN On-Premise Server (excluding TSO 500 pipelines)
  • Suited for advanced users looking to integrate DRAGEN pipelines into their existing cloud environment
DRAGEN On-Premise
View Video
DRAGEN-GATK Release Webinar

DRAGEN-GATK is a new best practices pipeline for secondary analysis of germline small variants, co-developed by the Broad Institute and Illumina. It combines the gold standard open-source GATK algorithms with the accuracy improvements from DRAGEN to ensure labs of all sizes and disciplines have access to high quality genomic analysis.

View Webinar Recording

Pioneering feline genetics with next-generation sequencing

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

Read Interview
Cloud-Based Computing: Speed and Scalability in a Cost-Efficient Environment

Kyle Retterer, MS, Chief Technology Officer of GeneDx, discusses how their company used Azure to scale their computing and data storage. This evolution brought more data analysis speed, infrastructure security, risk management, and simplicity to their data management.

Read Customer Spotlight
Reflections on a Long-term Collaboration to Drive Rapid Whole Genome Diagnostics

A rapid workflow with Illumina DNA PCR-Free Prep, NovaSeq 6000, and DRAGEN reduced turnaround time. The DRAGEN Platform was used to significantly increase the speed of mapping and aligning genomic data once sequenced.

Read Article
Using Genetic Testing to Advance Cancer Care

See how BaseSpace Sequence Hub and DRAGEN enabled easy-to-use, efficient workflows for NGS data analysis.

Read Article and Watch Video

Genetic Diseases

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


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


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

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

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Supporting Data and Figures

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