Publications and scientific evidence

Peer-reviewed validation of Genome Detective

Genome Detective is referenced in peer-reviewed scientific publications and used by leading research institutes, national reference laboratories, and public-health organizations.

This section provides access to scientific articles demonstrating the platform's accuracy, performance, and real-world value in pathogen genomics, outbreak response, and surveillance workflows.

Publications cover applications such as viral genomics, bacterial genomics, genomic epidemiology, and antimicrobial resistance analysis.

Genome Detective Tool

Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, et al. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics. 2019;35(5):871–3. View Publication

SARS-CoV-2 Related Papers

Cleemput S, Dumon W, Fonseca V, Abdool Karim W, et al. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. 2020;36(11):3552–5. View Publication

Carbo EC, Sidorov IA, Zevenhoven-Dobbe JC, Snijder EJ, et al. Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness. J Clin Virol. 2020 Oct 1;131:104594. View Publication

Tegally H, Wilkinson E, Lessells RJ, Giandhari J, et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med. 2021;27(3):440–6. View Publication

Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;10:1–6. View Publication

Viana R, Moyo S, Amoako DG, Tegally H, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. Jan 7;603(7902):679–86. View Publication

Citations of Interest

Ivens, M.J.R., Kamminga, S., Benchamach, K. et al. Rapid and reliable species-level identification from clinical samples using 16S rRNA gene nanopore sequencing analysis Sci Rep 15, 28606 (2025). View Publication

López-Labrador FX, Brown JR, Fischer N, Harvala H, et al. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. J Clin Virol. 2021;134:104691. View Publication

de Vries JJC, Brown JR, Couto N, Beer M, et al. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J Clin Virol. 2021;138:104812. View Publication

Boheemen S van, Rijn AL van, Pappas N, et al. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses. J Mol Diagnostics. 2020;22(2):196–207. View Publication

Fonseca V, Libin PJK, Theys K, Faria NR, et al. A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes. PLoS Negl Trop Dis. 2019;13(5):e0007231. View Publication

Chappell JG, Byaruhanga T, Tsoleridis T, et al. Identification of infectious agents in high-throughput sequencing data sets is easily achievable using free platforms. Journal of Clinical Microbiology. 2019;57. View Publication

Faria NR, Kraemer MUG, Hill SC, Jesus JG de, et al. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. 2018;361(6405):894–9. View Publication

Rijn AL van, Boheemen S van, Carbo EC, et al. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. bioRxiv. 2019;509919. View Publication

Pineda-Peña AC, Faria NR, Imbrechts S, et al. Automated subtyping of HIV-1 genetic sequences: Performance evaluation of REGA version 3 and seven other tools. Infect Genet Evol. 2013;19:337–48. View Publication

Kroneman A, Vennema H, Deforche K, et al. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol. 2011;51(2):121–5. View Publication