DRAGEN technical documentation
Find pipeline documentation, configuration references, parameter guidance, and application programming interface specifications for DRAGEN modules.
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DRAGEN secondary analysis
Call every true signal to discover more biology
Convert sequencing data into precise biological results
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10+ years
of continuous innovation
Up to 99.94%
F1 across all variant types
34 mins
FASTQ to VCF, 35× WGS
9.3M+
Genomes processed
The analytical foundation of BioInsight Platform
DRAGEN delivers accurate, comprehensive analysis across diverse variant types, with structured results ready for downstream research workflows.
Accuracy that improves with every release
Perform multigenome mapping, systematic noise-modeling, machine learning, and deep sequencing noise knowledge reduce errors across germline and somatic research workflows, including FFPE samples, without post-hoc filtering.
- ~90% germline error reduction across six DRAGEN releases1
- 4× PrecisionFDA challenge winner for germline and somatic analysis2
- 12× fewer errors than BWA-GATK in difficult-to-map regions3
- Significantly lower FFPE false positive rates (p = 5.7 × 10⁻¹¹ vs prior workflow)4
- Pangenome from 144 globally diverse samples (288 haplotypes), minimizes reference bias at scale3,5
Full spectrum biology in one software
Analyze SNVs, indels, structural variants, repeats, pharmacogenomics, HLA, biomarkers, RNA, and methylation without assembling separate tools or pipelines.
- Core variants: SNVs, indels, SVs, CNVs
- Repeat and structural: STR, ROH, UPD
- Specialty callers (13): HLA (41 genes), CYP2D6, GBA, SMN, LPA, and more
- Pharmacogenomics: 21 Tier-1 CPIC genes star-allele typed
- Biomarkers: TMB, MSI, HRD, mutational signatures
- RNA: Fusions, expression, PTD, UMI deduplication
- Methylation: 5-base, bisulfite, TAPS
- Somatic specialty: Focal amplification, purity/ploidy, oncovirus, FFPE-aware calling
Connect analysis to downstream workflows without reformatting
Send analysis outputs directly to Emedgene, Connected Multiomics, laboratory information management systems, and third-party interpretation platforms to generate structured results for review or downstream research without reformatting.
- Connected Multiomics
- Laboratory information management systems
- Third-party software
Simplify secondary analysis workflows
Install and validate DRAGEN once, then use a consistent command-line interface and software version across supported workflows to streamline pipeline management and maintenance.
Deploy where your data lives
Choose from five deployment models with bit-exact concordance, on FPGA, and standard CPU via DRAGEN SW-mode. Your data stays where your policies require, and your results never change.
Scale without limits
Process whole genomes in 34 minutes. Scale from pilot to population program without changing infrastructure.
Reference concordance
Get results that are natively comparable to UK Biobank and 1000 Genomes without reconciliation.
From reads to biological truth
One unified engine for every stage of secondary analysis, at any scale.
Process
Go from sequencing output and transform raw data into analysis-ready, accurately aligned reads.
Convert
Go from sequencer to reads with auto data ingest
Convert raw instrument data into analysis-ready reads without a separate tool or manual step. On-instrument or in the cloud, DRAGEN starts where the sequencer finishes.
Map and align
Use pangenome-anchored alignment that reduces bias
Align against 288 haplotypes from 144 globally diverse samples. Reduce false calls in difficult-to-map regions.
Analyze
Transform aligned sequencing data into biological measurements and assess the resulting data.
Call variants
Capture the complete variant landscape in one pass
Detect SNVs through biomarkers. Account for FFPE artifacts with modeling built into the caller and machine-learning models retrained with each release.
Multiomics
Measure multiomic features beyond variants
Quantify gene expression, RNA fusions, methylation, protein, cell-free DNA, and fragmentomic features within DRAGEN analysis workflows.
Quality control
Assess data quality within the analysis workflow
Evaluate coverage, contamination, and sex concordance without separate downstream quality control tools.
Deliver
Make results efficient to store and ready for downstream use.
Compress
Reduce storage needs with lossless compression
Compress sequencing data 5× more than gzip with DRAGEN-ORA, losslessly and without changing file compatibility. As your run volume grows, storage costs shrink proportionally.
Deliver
Deliver interpretation-ready results with no handoffs
Connect results automatically to Emedgene, Connected Multiomics, and Connected Annotations.
Support diverse research applications
Apply DRAGEN secondary analysis across human and nonhuman genomics applications.
Simple pricing that grows with you
Try the complete BioInsight Platform free for 30 days with no credit card, no purchase order, and no obligations. When you're ready to scale, pay only for what you use or choose the option to save with volume discounts.
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Explore DRAGEN resources
Access technical guidance, software updates, performance data, training, customer stories, and other resources for DRAGEN secondary analysis.
Review software updates, accuracy improvements, new variant callers, and performance enhancements.
Explore research publications evaluating DRAGEN accuracy, performance, and use across genomic applications.
Find product announcements, release highlights, upcoming events, recorded sessions, and updates from DRAGEN teams.
DRAGEN Iterative gVCF Genotyper (IGG)
Explore a breakthrough solution for population-scale variant analysis, with fast, efficient aggregation and genotyping of small germline variants across large cohorts.
Ready to call every signal?
Start with a free trial, schedule a demo, or speak with a specialist to configure DRAGEN for your infrastructure and workflows.
References
- Data on file
- precisionFDA. NCTR Indel Calling from Oncopanel Sequencing Data Challenge, Phases 1 and 2. 2022. precision.fda.gov/challenges/21; https://precision.fda.gov/challenges/22. Accessed September 15, 2026.
- Behera S, Catreux S, Rossi M, et al. Comprehensive genome analysis and variant detection at scale using DRAGEN. Nat Biotechnol. 2025;43(7):1177–1191. doi:10.1038/s41587-024-02382-1
- Tsuji J, Rickles-Young M, Abreu J, et al. Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling. Genom Med. 2026;11(1):31. doi:10.1038/s41525-026-00569-w
- Illumina. DRAGEN Bio-IT Platform documentation. help.dragen.illumina.com. Accessed September 15, 2026.