Read a selection of the published papers citing Genome Detective.
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. Birol I, editor. Bioinformatics. 2019;35(5):871–3. Available from: https://doi.org/10.1093/bioinformatics/bty695
Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LC, et al. Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes. Luigi Martelli P, editor. Bioinformatics. 2020;36(11):3552–5. Available from: https://doi.org/10.1093/bioinformatics/btaa145
Carbo EC, Sidorov IA, Zevenhoven-Dobbe JC, Snijder EJ, Claas EC, Laros JFJ, et al. Coronavirus discovery by metagenomic sequencing: a tool for pandemic preparedness. J Clin Virol. 2020 Oct 1;131:104594. Available from: https://doi.org/10.1016/j.jcv.2020.104594
Tegally H, Wilkinson E, Lessells RJ, Giandhari J, Pillay S, Msomi N, et al. Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med. 2021;27(3):440–6. Available from: https://doi.org/10.1038/s41591-021-01255-3
Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Detection of a SARS-CoV-2 variant of concern in South Africa. Nature. 2021;10:1–6. Available from: https://doi.org/10.1038/s41586-021-03402-9
Viana R, Moyo S, Amoako DG, Tegally H, Scheepers C, Althaus CL, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. Jan 7;603(7902):679–86. Available from: https://doi.org/10.1038/s41586-022-04411-y
López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, 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. Available from: https://doi.org/10.1016/j.jcv.2020.104691
de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, 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. Available from: https://doi.org/10.1016/j.jcv.2021.104812
Boheemen S van, Rijn AL van, Pappas N, Carbo EC, Vorderman RHP, Sidorov I, et al. Retrospective Validation of a Metagenomic Sequencing Protocol for Combined Detection of RNA and DNA Viruses Using Respiratory Samples from Pediatric Patients. J Mol Diagnostics. 2020;22(2):196–207. Available from: https://doi.org/10.1016/j.jmoldx.2019.10.007
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, 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. Available from: https://doi.org/10.1371/journal.pntd.0007231
Chappell JG, Byaruhanga T, Tsoleridis T, Ball JK, Patrick McClure C. Identification of infectious agents in high-throughput sequencing data sets is easily achievable using free, cloud-based bioinformatics platforms. Vol. 57, Journal of Clinical Microbiology. American Society for Microbiology; 2019. Available from: https://doi.org/10.1128/JCM.00466-19.
Faria NR, Kraemer MUG, Hill SC, Jesus JG de, Aguiar RS, Iani FCM, et al. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science. 2018;361(6405):894–9. Available from: https://science.sciencemag.org/content/361/6405/894
Rijn AL van, Boheemen S van, Carbo EC, Pappas N, Sidorov I, Mei H, et al. The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease. bioRxiv. 2019;509919. Available from: https://doi.org/10.1101/509919
Pineda-Peña AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol. 2013;19:337–48. Available from: https://doi.org/10.1016/j.meegid.2013.04.032
Kroneman A, Vennema H, Deforche K, Avoort H, Peñaranda S, Oberste MS, et al. An automated genotyping tool for enteroviruses and noroviruses. J Clin Virol. 2011;51(2):121–5. Available from: https://doi.org/10.1016/j.jcv.2011.03.006