Illumina DRAGEN Bio-IT Platform

The Illumina DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform provides accurate, ultra-rapid secondary genomic analysis of sequencing data. Read More...
The Illumina DRAGEN Bio-IT Platform offers
  • Accurate data: Detects small variants with high analytical sensitivity and specificity1
  • Robust speed: Processes an entire human genome at 30× coverage in about 25 minutes2,3
  • Frequent releases: Includes releases of regular enhancements and upgrades
  • Various applications: Analyzes next-generation sequencing (NGS) data from whole genomes, exomes, and RNA

The Illumina DRAGEN Bio-IT platform and data submission apps on BaseSpace Sequence Hub also support the SARS-CoV-2 Data Toolkit. Learn More.

DRAGEN Options
DRAGEN on BaseSpace Sequence Hub
DRAGEN on BaseSpace Sequence Hub
DRAGEN On-Premise
DRAGEN On-Premise
DRAGEN On-Premise
DRAGEN on NextSeq 1000/2000
Ultra-Rapid Secondary Genomic Analysis

The DRAGEN Platform can process NGS data for an entire human genome at 30× coverage in about 25 minutes on premise vs. > 15 hours with a traditional CPU-based system. It set two world speed records for genomic data analysis.2,3

Cost-Efficient Solution

When run on Illumina's BaseSpace Sequence Hub, analysis for a 30x genome is ~$5/sample and an exome at 100x coverage ~$3/sample.

Highly Accurate Results

In the 2018 PrecisionFDA Hidden Treasures – Warm Up Challenge, The DRAGEN Platform received the highest score in five out of six accuracy measures for whole-genome variant calling among platforms that recognized all 50 variants.1 Read the white paper to learn more.

Diverse Applications

The DRAGEN Platform analyzes sequencing data from a variety of experiment types, including whole genomes, whole exomes, germline and somatic datasets, and RNA sequencing experiments.

Frequent Updates

Frequent releases continuously expand and improve the DRAGEN Platform while accommodating new applications and addressing evolving industry standards. DRAGEN updates are version controlled, enabling users to opt in or out of new updates as desired.

Bringing Bioinformatics In-House Reduces Costs and Turnaround Time

Alexander Bisignano, cofounder and Chief Executive Officer of Phosphorus, discusses how the company uses the DRAGEN Bio-IT Platform to perform genomics data analysis onsite and at an accessible price point.

Read Interview
Phosphorus data analysis

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. 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 server DRAGEN BaseSpace NextSeq 1000/2000
Demultiplexing (BCL Convert)      
Map & Align      
RNA-Seq (gene fusion & quantification      
Exome enrichment (germline & somatic)     Germline only
Whole genome (germline & somatic)     Germline only
Methylation      
Joint Genotyping      
TSO 500 Liquid      
Metagenomics      

DRAGEN is also available via an Amazon Machine Image (AMI) on AWS MarketPlace

Pipeline Description Variant Types Detected Metrics Provided
DRAGEN Demultiplexing Rapid demultiplexing of NGS analysis N/A N/A
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
  • 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 using the DeSeq 2 app on BaseSpace Sequence Hub.
  • DNA fusion
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
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
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 BaseSpace Sequence Hub couples speed and accuracy of the DRAGEN Platform with the security, cost savings, and intuitive interface of BaseSpace Sequence Hub.

  • Push-button analysis for varying levels of expertise
  • Stream data directly from instruments for rapid analysis
  • Low costs with no hardware investments
  • Leverages the security, compliance, and storage features of BaseSpace Sequence Hub and Amazon Web Services (AWS)

Read Data Sheet

Learn More About BaseSpace Apps

DRAGEN on BaseSpace Sequence Hub
 

DRAGEN on-premise conducts secondary analysis in a fraction of the time compared with a traditional CPU-based system, while still maintaining high accuracy.

  • Analyze and store data locally
  • Supports varying levels of command line interface
  • Replace up to 30 traditional compute instances
  • Process NGS data for an entire human genome at 30x coverage in < 25 minutes
  • One unit supports two NovaSeq systems running at full capacity

Read Data Sheet

DRAGEN On-Premise
View Video
The Broad Institute

Collaborators Anthony Philippakis from The Broad Institute, and Susan Tousi of Illumina, discuss how integration of GATK with Illumina sequencers and implementation of the DRAGEN Platform may facilitate hardware acceleration and standardization of data analysis.

View Video
 

GeneDx Scales from Exomes to Genomes using DRAGEN

Leveraging DRAGEN, GeneDx is now able to grow its operations while keeping costs low, turnaround times short, and accuracy high.

Read Article
Rady Children’s Hospital

A Guinness world record was set for Fastest Genetic Diagnosis in 19.5 hours. The DRAGEN Platform was used to significantly increase the speed of mapping and aligning genomic data once sequenced.1

Read Article
Xing Cancer Care

See how Basespace Sequence Hub and DRAGEN have simplified NGS data analysis for this lab.

Watch Video

Read Article
Population Sequencing

Rapidly analyze the sequenced genomes; accelerate reanalysis as computational tools improve over time.

NICU and Genetic Disease Research

Reduce time required for genomic analysis, when fast results can be a critical factor.

Cancer Research

Accurate, rapid analysis of tumor-only and tumor/normal samples.

Agrigenomics

Analyze animals and plants of varying genomic complexities, using a provided reference.

Clinical and Translational Research

Analyze targeted exome data with rapid turnaround and high accuracy to ensure reproducibility and high-quality results.

References
  1. Precision FDA Hidden Treasures Warm Up. precision.fda.gov/challenges/1/view/results. Accessed September 14, 2018.
  2. Bio IT World. Children’s Hospital Of Philadelphia, Edico Set World Record For Secondary Analysis Speed. October 23, 2017. www.bio-itworld.com/2017/10/23/childrens-hospital-of-philadelphia-edico-set-world-record-for-secondary-analysis-speed.aspx. Accessed September 19, 2018.
  3. The San Diego Union Tribune. Rady Children's Institute sets Guinness world record. February 12, 2018. www.sandiegouniontribune.com/news/health/sd-no-rady-record-20180209-story.html. Accessed September 19, 2018.

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