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

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

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