000K utf8 1100 2024$c2024-06-28 1500 eng 2050 urn:nbn:de:hbz:465-20250228-130358-9 2051 10.1186/s12864-024-10539-0 3000 Thomas, Alexander 3010 Anastasiou, Olympia 3010 Battenfeld, Thomas 3010 Dittmer, Ulf 3010 Dörr, Adrian 3010 Dörr, Ann-Kathrin 3010 Elsner, Carina 3010 Gosch, Jule 3010 Köster, Johannes 3010 Kraiselburd, Ivana 3010 Le-Trilling, Vu Thuy Khanh 3010 Magin, Simon 3010 Meyer, Folker 3010 Schöler, Lara 3010 Scholtysik, René 3010 Trilling, Mirko 3010 Yilmaz, Pelin 4000 UnCoVar$dA reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example [Thomas, Alexander] 4209 Background: At a global scale, the SARS-CoV-2 virus did not remain in its initial genotype for a long period of time, with the first global reports of variants of concern (VOCs) in late 2020. Subsequently, genome sequencing has become an indispensable tool for characterizing the ongoing pandemic, particularly for typing SARS-CoV-2 samples obtained from patients or environmental surveillance. For such SARS-CoV-2 typing, various in vitro and in silico workflows exist, yet to date, no systematic cross-platform validation has been reported. Results: In this work, we present the first comprehensive cross-platform evaluation and validation of in silico SARS-CoV-2 typing workflows. The evaluation relies on a dataset of 54 patient-derived samples sequenced with several different in vitro approaches on all relevant state-of-the-art sequencing platforms. Moreover, we present UnCoVar, a robust, production-grade reproducible SARS-CoV-2 typing workflow that outperforms all other tested approaches in terms of precision and recall. Conclusions: In many ways, the SARS-CoV-2 pandemic has accelerated the development of techniques and analytical approaches. We believe that this can serve as a blueprint for dealing with future pandemics. Accordingly, UnCoVar is easily generalizable towards other viral pathogens and future pandemics. The fully automated workflow assembles virus genomes from patient samples, identifies existing lineages, and provides high-resolution insights into individual mutations. UnCoVar includes extensive quality control and automatically generates interactive visual reports. UnCoVar is implemented as a Snakemake workflow. The open-source code is available under a BSD 2-clause license at github.com/IKIM-Essen/uncovar. 4950 https://doi.org/10.1186/s12864-024-10539-0$xR$3Volltext$534 4950 https://nbn-resolving.org/urn:nbn:de:hbz:465-20250228-130358-9$xR$3Volltext$534 4961 https://duepublico2.uni-due.de/receive/duepublico_mods_00082415 5051 610 5550 Lineage assignment 5550 Next generation sequencing 5550 SARS-CoV-2 5550 Variant calling 5550 Workflow