DRAGEN
Illumina Connected Software
  • Overview
    • Illumina® DRAGEN™ Secondary Analysis
    • DRAGEN Applications
    • Deployment Options
  • Product Guides
    • DRAGEN v4.4
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • Clinical Research Workflows
        • DRAGEN Heme WGS Tumor Only Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
        • DRAGEN Solid WGS Tumor Normal Pipeline
          • Quick Start
          • Sample Sheets
            • Introduction
            • Requirements
            • Templates
          • Run Planning
            • Sample Sheet Creation in BaseSpace
            • Custom Config Support
          • DRAGEN Server App
            • Quick Start
            • Getting Started
            • Launching Analysis
            • Command Line Options
            • Output
            • Advanced Topics
            • Custom Workflow
              • Custom Config Support
            • Illumina Connected Insights
          • ICA Cloud App
            • Getting Started
            • Launching Analysis
            • Output
            • Advanced Topics
              • Custom Workflow
              • Custom Config Support
              • Post Processing
              • Illumina Connected Insights
          • Analysis Output
          • Analysis Methods
          • Troubleshooting
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • Illumina scRNA
        • Other scRNA prep
        • RNA Panel
        • RNA WTS
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Pedigree Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • Available pipelines
            • Germline CNV Calling (WGS/WES)
            • Germline CNV Calling ASCN (WGS)
            • Multisample Germline CNV Calling
            • Somatic CNV Calling ASCN (WGS)
            • Somatic CNV Calling WES
            • Somatic CNV Calling ASCN (WES)
          • Additional documentation
            • CNV Input
            • CNV Preprocessing
            • CNV Segmentation
            • CNV Output
            • CNV ASCN module
            • CNV with SV Support
            • Cytogenetics Modality
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
          • Structural Variant IGV Tutorial
        • VNTR Calling
        • Population Genotyping
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • JSON Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single Cell Pipeline
        • Illumina PIPseq scRNA
        • Other scRNA Prep
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN MRD Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
        • Docker Requirements
      • DRAGEN Reports
      • Tools and Utilities
    • DRAGEN v4.3
      • Getting Started
      • DRAGEN Host Software
        • DRAGEN Secondary Analysis
      • DRAGEN Reference Support
        • Prepare a Reference Genome
      • DRAGEN DNA Pipeline
        • DNA Mapping
        • Read Trimming
        • DRAGEN FASTQC
        • Sorting and Duplicate Marking
        • Small Variant Calling
          • ROH Caller
          • B-Allele Frequency Output
          • Somatic Mode
          • Joint Analysis
          • De Novo Small Variant Filtering
          • Autogenerated MD5SUM for VCF Files
          • Force Genotyping
          • Machine Learning for Variant Calling
          • Evidence BAM
          • Mosaic Detection
          • VCF Imputation
          • Multi-Region Joint Detection
        • Copy Number Variant Calling
          • CNV Output
          • CNV with SV Support
          • Multisample CNV Calling
          • Somatic CNV Calling WGS
          • Somatic CNV Calling WES
          • Allele Specific CNV for Somatic WES CNV
        • Repeat Expansion Detection
          • De Novo Repeat Expansion Detection
        • Targeted Caller
          • CYPDB6 Caller
          • CYP2D6 Caller
          • CYP21A2 Caller
          • GBA Caller
          • HBA Caller
          • LPA Caller
          • Rh Caller
          • SMN Caller
        • Structural Variant Calling
          • Structural Variant De Novo Quality Scoring
        • VNTR Calling
        • Filter Duplicate Variants
        • Ploidy Calling
          • Ploidy Estimator
          • Ploidy Caller
        • Multi Caller
        • QC Metrics Reporting
        • HLA Typing
        • Biomarkers
          • Tumor Mutational Burden
          • Microsatellite Instability
          • Homologous Recombination Deficiency
          • BRCA Large Genomic Rearrangment
          • DRAGEN Fragmentomics
        • Downsampling
          • Fractional (Raw Reads) Downsampling
          • Effective Coverage Downsampling
        • Unique Molecular Identifiers
        • Indel Re-aligner (Beta)
        • Star Allele Caller
        • High Coverage Analysis
        • CheckFingerprint
        • Population Haplotyping (Beta)
        • DUX4 Rearrangement Caller
      • DRAGEN RNA Pipeline
        • RNA Alignment
        • Gene Fusion Detection
        • Gene Expression Quantification
        • RNA Variant Calling
        • Splice Variant Caller
      • DRAGEN Single-Cell Pipeline
        • scRNA
        • scATAC
        • Single-Cell Multiomics
      • DRAGEN Methylation Pipeline
      • DRAGEN Amplicon Pipeline
      • Explify Analysis Pipeline
        • Kmer Classifier
        • Kmer Classifier Database Builder
      • DRAGEN Recipes
        • DNA Germline Panel UMI
        • DNA Germline Panel
        • DNA Germline WES UMI
        • DNA Germline WES
        • DNA Germline WGS UMI
        • DNA Germline WGS
        • DNA Somatic Tumor-Normal Solid Panel UMI
        • DNA Somatic Tumor-Normal Solid Panel
        • DNA Somatic Tumor-Normal Solid WES UMI
        • DNA Somatic Tumor-Normal Solid WES
        • DNA Somatic Tumor-Normal Solid WGS UMI
        • DNA Somatic Tumor-Normal Solid WGS
        • DNA Somatic Tumor-Only Heme WGS
        • DNA Somatic Tumor-Only Solid Panel UMI
        • DNA Somatic Tumor-Only Solid Panel
        • DNA Somatic Tumor-Only Solid WES UMI
        • DNA Somatic Tumor-Only Solid WES
        • DNA Somatic Tumor-Only Solid WGS UMI
        • DNA Somatic Tumor-Only Solid WGS
        • DNA Somatic Tumor-Only ctDNA Panel UMI
        • RNA Panel
        • RNA WTS
      • BCL conversion
      • Illumina Connected Annotations
      • ORA Compression
      • Command Line Options
      • DRAGEN Reports
      • Tools and Utilities
  • Reference
    • DRAGEN Server
    • DRAGEN Multi-Cloud
      • DRAGEN on AWS
      • DRAGEN on AWS Batch
      • DRAGEN on Microsoft Azure
        • Run DRAGEN VM on Azure
      • DRAGEN on Microsoft Azure Batch
        • Azure Batch Run Modes
    • DRAGEN Licensing
      • DRAGEN Server Licensing
      • DRAGEN Cloud Licensing
    • DRAGEN Application Manager
    • Support
    • Resource Files
      • Noise Baselines
    • Supplementary Information
    • Troubleshooting
    • Citing DRAGEN software
    • Release Notes
    • Revision History
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On this page
  • Method 1: Cite DRAGEN secondary analysis software in-text or in reference/bibliography list
  • In-text
  • Reference or bibliography list
  • Method 2: Cite a specific algorithm using one of the papers listed below
  • DRAGEN Germline Algorithms
  • Germline CNV Caller
  • Somatic CNV Caller
  • STR Expansion Detection
  • LPA Targeted Caller
  • SMN Targeted Caller
  • CYP2D6 Targeted Caller
  • GBA Targeted Caller
  • DUX4 Rearrangements Caller

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  1. Reference

Citing DRAGEN software

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Last updated 2 days ago

Was this helpful?

There are two preferred methods to cite DRAGEN software.

Method 1: Cite DRAGEN secondary analysis software in-text or in reference/bibliography list

In-text

Proper in-text citation for DRAGEN software must include the Illumina DRAGEN software product used and the version number at the time of data analysis.

Example

Secondary analysis was performed using Illumina DRAGEN software, v4.3.

Reference or bibliography list

Citing DRAGEN software in a bibliography or reference list should include the company name, copyright date, name of the DRAGEN software product, version number, format, and link to product website.

Example

Illumina (2024). DRAGEN secondary analysis (Version 4.3) [Computer software].

Method 2: Cite a specific algorithm using one of the papers listed below

DRAGEN Germline Algorithms

Behera, S., Catreux, S., Rossi, M. et al., Comprehensive genome analysis and variant detection at scale using DRAGEN, Nat Biotechnol (2024).

Germline CNV Caller

Somatic CNV Caller

STR Expansion Detection

LPA Targeted Caller

SMN Targeted Caller

CYP2D6 Targeted Caller

GBA Targeted Caller

DUX4 Rearrangements Caller

De La Vega, F.M., et al., Benchmarking of Germline Copy Number Variant Callers from Whole Genome Sequencing Data for Clinical Applications, Bioinformatics Advances (2025).

Masood, D., Ren, L., Nguyen, C., Brundu, F.G., Zheng, L. et al., Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome, Genome Biology, 25(1), 163 (2024).

Dolzhenko et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res. 2017 Nov;27(11):1895-1903.

Dolzhenko, E. et al., ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions, Bioinformatics, Volume 35, Issue 22, November 2019, Pages 4754–4756,

Dolzhenko, E., Bennett, M.F., Richmond, P.A. et al. ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data. Genome Biol 21, 102 (2020).

Behera, S., Belyeu, J.R., Chen, X. et al., Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk, BMC Med Genomics 17, 255 (2024).

Chen, X., Sanchis-Juan, A., French, C.E. et al., Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data, Genet Med 22, 945–953 (2020).

Chen, X., Shen, F., Gonzaludo, N. et al., Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data, Pharmacogenomics J 21, 251–261 (2021).

Toffoli, M., Chen, X., Sedlazeck, F.J. et al., Comprehensive short and long read sequencing analysis for the Gaucher and Parkinson’s disease-associated GBA gene, Commun Biol 5, 670 (2022).

Grobecker, P., Berri, S., Peden, J.F. et al. A dedicated caller for DUX4 rearrangements from whole-genome sequencing data. BMC Med Genomics 18, 24 (2025).

https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html
https://doi.org/10.1038/s41587-024-02382-1
https://doi.org/10.1093/bioadv/vbaf071
https://doi.org/10.1186/s13059-024-03294-8
https://doi.org/10.1101/gr.225672.117
https://doi.org/10.1093/bioinformatics/btz431
https://doi.org/10.1186/s13059-020-02017-z
https://doi.org/10.1186/s12920-024-02024-0
https://doi.org/10.1038/s41436-020-0754-0
https://doi.org/10.1038/s41397-020-00205-5
https://doi.org/10.1038/s42003-022-03610-7
https://doi.org/10.1186/s12920-024-02069-1