Single next-generation sequencing (NGS) proved to be an important tool for monitoring the SARS-CoV-2 outbreak at the global level Until today, thousands of SARS-CoV-2 genome sequences have been published at GISAID (Global Initiative on Sharing All Influenza Data) but only a portion are suitable for reliable variant analysis. Here we report on the comparison of three commercially available NGS library preparation kits. We discuss advantages and limitations from the perspective of required input sample quality and data quality for advanced SARS-CoV-2 genome analysis.

Department of Biology and Medical Genetics 2nd Faculty of Medicine Charles University and Motol University Hospital 5 Úvalu 84 150 06 Prague Czech Republic

Faculty of Science Charles University Albertov 6 128 00 Prague Czech Republic

Institute of Applied Biotechnologies Služeb 3056 4 108 00 Prague Czech Republic

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