# Citing DRAGEN software

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]. [https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html](file:///Users/mdelrosar1/Library/CloudStorage/OneDrive-Illumina,Inc/Documents/22_Documentation/Gitbook/%22)

## 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). <https://doi.org/10.1038/s41587-024-02382-1>

### Germline CNV 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). <https://doi.org/10.1093/bioadv/vbaf071>

Gao, Y., *et al.*, Whole-Genome Sequencing is a Viable Replacement for Chromosomal Microarray and Fragile X PCR Testing, *medRxiv* (2025): 2025-05. <https://doi.org/10.1101/2025.05.24.25328260>

### Somatic CNV Caller

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). <https://doi.org/10.1186/s13059-024-03294-8>

### STR Expansion Detection

Dolzhenko et al. Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res. 2017 Nov;27(11):1895-1903. <https://doi.org/10.1101/gr.225672.117>

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, <https://doi.org/10.1093/bioinformatics/btz431>

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). <https://doi.org/10.1186/s13059-020-02017-z>

### LPA Targeted Caller

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). <https://doi.org/10.1186/s12920-024-02024-0>

### SMN Targeted Caller

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). <https://doi.org/10.1038/s41436-020-0754-0>

### CYP2D6 Targeted Caller

Chen, X., Shen, F., Gonzaludo, N. *et al.*, Cyrius: accurate *CYP2D6* genotyping using whole-genome sequencing data, *Pharmacogenomics J* **21**, 251–261 (2021). <https://doi.org/10.1038/s41397-020-00205-5>

### GBA Targeted Caller

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). <https://doi.org/10.1038/s42003-022-03610-7>

### DUX4 Rearrangements Caller

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://doi.org/10.1186/s12920-024-02069-1>


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