Informatics Products

DRAGEN secondary analysis

Accurate, comprehensive, efficient analysis

A suite of bioinformatics pipelines to process NGS data and maximize genomic discovery

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Meet Illumina DRAGEN

Illumina DRAGEN (Dynamic Read Analysis for GENomics) secondary analysis enables labs of all sizes and disciplines to maximize the value of the genome with powerful, cutting-edge data analysis tools. DRAGEN secondary analysis provides accurate, comprehensive, and highly efficient bioinformatics with multiple deployment options, applications, and pipelines to meet your research needs. 

Key features and benefits

Accurate results

Confidently analyze with exceptionally accurate results. DRAGEN achieved a 99.90% accuracy1 score using the Precision FDA Truth Challenge v2 benchmark data.

Comprehensive solution

Analyze whole genomes, exomes, methylomes, and transcriptomes with a single solution that replaces up to 30 open-source tools.  

Efficient analysis

Process a 40× genome in ~ 34 min, with all supported callers.2 Reduce FASTQ file sizes up to 5× with DRAGEN ORA compression. DRAGEN secondary analysis resulted in two world speed records for genomic data analysis.3,4

Cost efficiency

Built-in lossless data compression decreases storage costs by 80%5. Preconfigured workflows reduce time and expense for developing and maintaining analysis pipelines.


Multiplatform accessibility

Meeting you where your data and expertise is. DRAGEN secondary analysis is available via on-premises server, in the cloud, or directly onboard the NovaSeq X Series, NextSeq 1000 and NextSeq 2000 Systems, and the MiSeq i100 Series.

Streamlined integration

Easily integrate with Illumina sequencers, enabling a streamlined workflow from sequencing to downstream tertiary analysis.

Deployment options

Access DRAGEN secondary analysis via an on-premises server, cloud-based, or on-instrument solution. Multiple deployment options support your analysis needs without compromising accuracy, speed, or flexibility. 

View deployment options

Key analysis apps and pipelines

DRAGEN secondary analysis supports an extensive range of applications, providing comprehensive coverage for many experiment types in a single solution. Key applications include:  

  • Germline (whole-genome and enrichment)
  • Somatic (whole-genome and enrichment, tumor-only and tumor-normal)
  • RNA
  • Methylation

DRAGEN secondary analysis includes a versatile set of pipelines that can accept input data files and create output files at different stages of the pipelines. 

View apps and pipelines
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DRAGEN IGG: Powering population-scale variant discovery

The DRAGEN Iterative gVCF Genotyper (IGG) delivers a breakthrough solution for population-scale variant analysis, enabling fast, efficient aggregation and genotyping of small germline variants across large cohorts. Designed for speed, accuracy, and scalability, IGG supports incremental analysis so new sample batches can be added without reprocessing the entire dataset.

Learn more

In our hands, using DRAGEN [secondary] analysis, we have realized cost savings of approximately 50%. In terms of computational time, it’s almost double the speed compared to the manual method.

Dr Damian Kao Chief Operating Officer Basepaws
Read article

Advances using DRAGEN secondary analysis

From genetic diseases to oncology to pharmacogenomics and more, DRAGEN secondary analysis can help labs in any field scale up NGS operations and make game-changing genomic analysis a reality.

Featured resources

Comprehensive coverage with leading edge innovations

DRAGEN v4.4 is here with powerful innovations for genomic and multiomic analysis.

This release introduces new oncology applications for Heme WGS, Solid WGS tumor-normal, and a streamlined pipeline for Minimal Residual Disease (MRD). It also delivers optimized secondary analysis for the latest assays and major accuracy gains in germline and somatic pipelines, including improved structural variant calling.

Watch the on-demand webinar to explore all the new features and see how DRAGEN v4.4 accelerates your journey from samples to insights.

Watch webinar

Learn more or get in touch

View more details about DRAGEN secondary analysis features, learn how to order, and find product documentation. You can also speak to a specialist to get your questions answered. 

See more product details

References

  1. Illumina internal data on file, 2025, accuracy score calculated with DRAGEN v4.4 using benchmark data from Precision FDA Truth Challenge v2 https://precision.fda.gov/challenges/10
  2. Illumina internal data on file, 2024. Run time calculated using DRAGEN v4.3 on DRAGEN server v4. Includes calling Full suite of callers for structural variants, repeat expansions, and targeted callers.
  3. BioIT World. Children’s Hospital of Philadelphia, Edico set world record for secondary analysis speed. bio-itworld.com/ news/2017/10/23/children-s-hospital-of-philadelphia-edico-set-world-record-for-secondary-analysis-speed. Published October 23, 2017. Accessed March 14, 2022.
  4. San Diego Union Tribune. Rady Children’s Institute sets Guinness world record. sandiegouniontribune.com/95899028-132.html. Published February 12, 2018. Accessed March 14, 2022.