Illumina DRAGEN secondary analysis ordering

Maximize genomic insights with DRAGEN secondary analysis, learn about the latest updates, read FAQs, and find product support.

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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 ~34 min with DRAGEN v4.3, calling a wide range of variants (SNV, indel, CNV, SV, mosaic variants, star alleles, etc.) vs 8 hours with a traditional open source solution calling fewer variant types

  • Reduce FASTQ file sizes up to 5× with DRAGEN Original Read Archive (ORA)

  • Drive unprecedented accuracy with multigenome (graph) reference genome and machine learning

Overcome challenges in genomic analysis

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.

Access a broad range of applications and pipelines

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 Systems.

Seamlessly integrate DRAGEN analysis pipelines with somatic oncology variant interpretation using Connected Insights on-premise via DRAGEN server.


Specifications


Software updates

DRAGEN v4.3 is now available on-premises and on-cloud

  • Next-generation multigenome mapper that incorporates hundreds of high-quality reference samples improving variant calling accuracy and reducing ethnicity bias

  • New integrated mosaic variant caller powered by specialized machine learning model for detecting mosaic variants with low allele frequency

  • New specialized caller - Multi-Region Joint Detection (MRJD) caller for genotyping of medically relevant genes such as PMS2, SMN1, SMN2, STRC, NEB, TTN, IKBKG in challenging segmental duplication regions

  • Expanded ORA compression capability to support human methylation data and non-human data

DRAGEN v4.2 is now available onboard NextSeq 1000 and NextSeq 2000 Series:

  • Enhanced multigenome (graph) reference and Machine Learning (ML) models improves variant calling accuracy

  • Accurate PGx genotyping with new targeted callers and star allele caller

  • Comprehensive coverage with expanded catalog of repeat expansions, increased support for sex chromosome low allele frequency variants, and enhanced bulk-rna QC metrics

DRAGEN v4.1 available onboard NovaSeq X Series

  • Provides variant calling and up to 5× lossless data compression with Original Read Archive (ORA)

  • Runs multiple secondary analysis pipelines in parallel

  • Includes BCL Convert, Germline, RNA, Enrichment, Somatic and Methylation application options

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

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DRAGEN secondary analysis
Accurate, comprehensive, and efficient analysis of NGS data.

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Insights

Related applications and methods

Key DRAGEN applications and availability

Application DRAGEN On-Premises Server NovaSeq X Series NextSeq 1000/2000 BaseSpace Sequence Hub Illumina Connected Analytics
BCL Convert
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custom only
DRAGEN ORA Compression
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custom only
DRAGEN FASTQ + MultiQC
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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 Germline + somatic Germline + somatic Germline + somatic
DRAGEN Amplicon
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  DNA only
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RNA
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Single-Cell RNA
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NanoString GeoMx NGS (spatial transcriptomics)    
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Methylation
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Metagenomics      
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COVID COVIDSeq, COVID lineage   COVIDSeq (cloud only) COVIDSeq, COVID lineage  
TruSight Oncology 500
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ScATAC-Seq (single-cell sequencing assay for transposase-accessible chromatin)
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Imputation
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PGx Star Allele Caller
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Illumina Complete Long Reads      
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RPIP and UPIP panels Beta    
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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

Pipeline Description Variant types detected Metrics provided
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
  • Compression Ratio
  • Run Time
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 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
  • Indel
  • CNV
  • SV
  • Repeat Expansions
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
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.
  • SNV
  • Indel
  • CNV
  • SV
  • TMB
  • MSI
  • HLA
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
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.
  • SNV
  • Indel
  • CNV
  • SV
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
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).
  • Gene fusion
  • SNV
  • Indel
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
DRAGEN Single Cell RNA 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 Calls variants jointly across multiple genomes and scales to large cohorts of samples at expedited speeds with uncompromising accuracy.
  • SNV
  • Indel
  • CNV
  • SV
  • Repeat Expansions
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
DRAGEN Methylation Performs alignment and methyl calling. 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 Offers secondary analysis support for TruSight Oncology 500 ctDNA. Only available on the local DRAGEN Server (version 3).
  • SNV
  • Indel
  • CNV
  • DNA fusions
  • MSI
  • TMB
  • Mapping metrics
  • Duration Metrics
  • Coverage Metrics
  • Variant Metrics
  • Callability Report
DRAGEN Imputation Enables scalable low-pass whole-genome sequencing analysis in an end-to-end user-friendly tool.
  • SNV
  • Indel
N/A
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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.

Documentation

Product literature

Figures

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.

dragen multiplatform accessibility

Multiplatform accessibility

DRAGEN analysis pipeline access options with features designed to fit the NGS analysis needs of every lab.

dragen on basespace sequence hub

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.

Explore example data sets

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

Resources

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Meet Illumina DRAGEN secondary analysis

DRAGEN offers accurate, comprehensive, and efficient secondary analysis of NGS data.

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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.

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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.

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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.

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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.

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

Illumina DRAGEN Server v4

20051343

Includes Advance Exchange support for the first year. Requires purchase of annual DRAGEN license.

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DRAGEN Server Lvl 1 1 year License

20060397

Throughput of 100,000 Gb on DRAGEN Server

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DRAGEN Server Lvl 2 1 year License

20060398

Throughput of 250,000 Gb on DRAGEN Server

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DRAGEN Server Lvl 3 1 year License

20060399

Throughput of 500,000 Gb on DRAGEN Server

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DRAGEN Server Lvl 4 1 year License

20060400

Througput of 1,000,000 Gb on DRAGEN Server

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DRAGEN Server Lvl 5 1 year License

20060401

Throughput of 2,000,000 Gb on DRAGEN Server

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FAQ

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.

/ Results

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

References

  1.     Miller NA, Farrow EG, Gibson M, et al. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med. 2015;7:100. doi: 10.1186/s13073-015-0221-8
  2.     Illumina. DRAGEN sets new standard for data accuracy in PrecisionFDA benchmark data. Optimizing variant calling performance with Illumina machine learning and DRAGEN graph. https://www.illumina.com/science/genomics-research/articles/dragen-shines-again-precisionfda-truth-challenge-v2.html. Accessed March 22, 2023.

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