DRAGEN secondary analysis

Accurate, comprehensive, efficient analysis

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


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 99.89% accuracy score using the Precision FDA Truth Challenge v2 benchmark data.1

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 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 NextSeq 1000 and NextSeq 2000 Sequencing Systems and the NovaSeq X Series.

Streamlined integration

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

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. 

woman on a computer

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. 

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

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

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. 


  1. Illumina. DRAGEN sets new standard for data accuracy in PrecisionFDA benchmark data. Optimizing variant calling performance with Illumina machine learning and DRAGEN graph. illumina.com/science/genomics-research/articles/dragen-shines-again-precisionfda-truth-challenge-v2.html. Accessed March 22, 2023.
  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.