There are two preferred methods to cite DRAGEN software.
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.
Secondary analysis was performed using Illumina DRAGEN software, v4.3.
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.
Illumina (2024). DRAGEN secondary analysis (Version 4.3) [Computer software]. https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html
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
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
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
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
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
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
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
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
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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