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Preprint

Sequencing data processing and analysis

AP Alexandra Popa
JG Jakob-Wendelin Genger
AB Andreas Bergthaler

Last updated date: Dec 22, 2020 Views: 971 Forks: 0

original An abbreviated version of this protocol was published in Science Translational Medicine in Dec, 2020
Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2
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All our data and scripts from raw to figure generation are provided online here:

https://www.sarscov2-austria.org/our-publications/popa-genger-2020/


For the viral genome assembly in particular please check here:

https://github.com/Bergthalerlab/SARSCoV2_Code/

in the file: 

SarsVirSeq_VariantCaller.py

Copyright: Content may be subjected to copyright.
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Popa, A, Genger, J and Bergthaler, A(2020). Sequencing data processing and analysis. Bio-protocol Preprint. bio-protocol.org/prep714.
  2. 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

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