Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:

Popa, A, Genger, J and Bergthaler, A(2020). Sequencing data processing and analysis. Bio-protocol Preprint. bio-protocol.org/prep714.
Popa, A., Genger, J., Nicholson, M. D., Penz, T., Schmid, D., Aberle, S. W., Agerer, B., Lercher, A., Endler, L., Colaço, H., Smyth, M., Schuster, M., Grau, M. L., Martínez-Jiménez, F., Pich, O., Borena, W., Pawelka, E., Keszei, Z., Senekowitsch, M., Laine, J., Aberle, J. H., Redlberger-Fritz, M., Karolyi, M., Zoufaly, A., Maritschnik, S., Borkovec, M., Hufnagl, P., Nairz, M., Weiss, G., Wolfinger, M. T., Laer, D. V., Superti-Furga, G., Lopez-Bigas, N., Puchhammer-Stöckl, E., Allerberger, F., Michor, F., Bock, C. and Bergthaler, A.(2020). Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Science Translational Medicine 12(573). DOI: 10.1126/scitranslmed.abe2555