Primary

Posada-Céspedes, Susana, David Seifert, Ivan Topolsky, Kim Philipp Jablonski, Karin J Metzner, and Niko Beerenwinkel. 2021. “V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data.” Bioinformatics, January. https://doi.org/10.1093/bioinformatics/btab015.

General

Hufsky, Franziska, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia Arighi, Alex Bateman, Jan Baumbach, et al. 2020. “Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research.” Preprints. https://doi.org/10.20944/preprints202005.0376.v1.
Ibrahim, Bashar, Ksenia Arkhipova, Arno C. Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene V. Koonin, et al. 2018. “Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting.” Viruses 10 (5). https://doi.org/10.3390/v10050256.
Posada-Céspedes, Susana, David Seifert, and Niko Beerenwinkel. 2017. “Recent Advances in Inferring Viral Diversity from High-Throughput Sequencing Data.” Virus Research 239: 17–32. https://doi.org/10.1016/j.virusres.2016.09.016.

Use of V-pipe

Alm, Erik, Eeva K Broberg, Thomas Connor, Emma B Hodcroft, Andrey B Komissarov, Sebastian Maurer-Stroh, Angeliki Melidou, et al. 2020. “Geographical and Temporal Distribution of SARS-CoV-2 Clades in the WHO European Region, January to June 2020.” Eurosurveillance 25 (32). https://doi.org/10.2807/1560-7917.es.2020.25.32.2001410.
Bagutti, Claudia, Monica Alt Hug, Philippe Heim, Laura Maurer Pekerman, Evelyn Ilg Hampe, Philipp Hübner, Simon Fuchs, et al. 2022. “Wastewater Monitoring of SARS-CoV-2 Shows High Correlation with COVID-19 Case Numbers and Allowed Early Detection of the First Confirmed b.1.1.529 Infection in Switzerland: Results of an Observational Surveillance Study.” Swiss Medical Weekly 152 (2526): w30202. https://doi.org/10.4414/SMW.2022.w30202.
Carlisle, Louisa A, Teja Turk, Katharina Kusejko, Karin J Metzner, Christine Leemann, Corinne D Schenkel, Nadine Bachmann, et al. 2019. “Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection.” The Journal of Infectious Diseases, April. https://doi.org/10.1093/infdis/jiz094.
Chen, Chaoran, Sarah Ann Nadeau, Ivan Topolsky, Marc Manceau, Jana S. Huisman, Kim Philipp Jablonski, Lara Fuhrmann, et al. 2021. “Quantification of the Spread of SARS-CoV-2 Variant b.1.1.7 in Switzerland.” Epidemics 37: 100480. https://doi.org/10.1016/j.epidem.2021.100480.
Klaus, Julia, Marina Meli, Barbara Willi, Sarah Nadeau, Christian Beisel, Tanja Stadler, Herman Egberink, et al. 2021. “Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland.” Viruses 13 (3): 496. https://doi.org/10.3390/v13030496.
Kuhlmeier, Evelyn, Tatjana Chan, Cecilia Valenzuela Agüí, Barbara Willi, Aline Wolfensberger, Christian Beisel, Ivan Topolsky, et al. 2023. “Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland.” Viruses 15 (1). https://doi.org/10.3390/v15010245.
Kuipers, Jack, Aashil A Batavia, Kim Philipp Jablonski, Fritz Bayer, Nico Borgsmüller, Arthur Dondi, Monica-Andreea Drăgan, et al. 2020. “Within-Patient Genetic Diversity of SARS-CoV-2.” bioRxiv. https://doi.org/10.1101/2020.10.12.335919.
Nadeau, Sarah A., Timothy G. Vaughan, Christiane Beckmann, Ivan Topolsky, Chaoran Chen, Emma Hodcroft, Tobias Schär, et al. 2023. “Swiss Public Health Measures Associated with Reduced SARS-CoV-2 Transmission Using Genome Data.” Science Translational Medicine 15 (680): eabn7979. https://doi.org/10.1126/scitranslmed.abn7979.
Nadeau, Sarah, Christiane Beckmann, Ivan Topolsky, Timothy Vaughan, Emma Hodcroft, Tobias Schär, Ina Nissen, et al. 2020. “Quantifying SARS-CoV-2 Spread in Switzerland Based on Genomic Sequencing Data.” medRxiv. https://doi.org/10.1101/2020.10.14.20212621.

Components of V-pipe developed at CBG-ETHZ

Dreifuss, David, Ivan Topolsky, Pelin Icer Baykal, and Niko Beerenwinkel. 2022. “Tracking SARS-CoV-2 Genomic Variants in Wastewater Sequencing Data with LolliPop.” medRxiv. https://doi.org/10.1101/2022.11.02.22281825.
Fuhrmann, Lara, Kim Philipp Jablonski, and Niko Beerenwinkel. 2021. “Quantitative Measures of Within-Host Viral Genetic Diversity.” Current Opinion in Virology 49: 157–63. https://doi.org/10.1016/j.coviro.2021.06.002.
Jahn, Katharina, David Dreifuss, Ivan Topolsky, Anina Kull, Pravin Ganesanandamoorthy, Xavier Fernandez-Cassi, Carola Bänziger, et al. 2021. “Detection and Surveillance of SARS-CoV-2 Genomic Variants in Wastewater.” medRxiv. https://doi.org/10.1101/2021.01.08.21249379.
McElroy, Kerensa, Osvaldo Zagordi, Rowena Bull, Fabio Luciani, and Niko Beerenwinkel. 2013. “Accurate Single Nucleotide Variant Detection in Viral Populations by Combining Probabilistic Clustering with a Statistical Test of Strand Bias.” BMC Genomics 14 (1): 501. https://doi.org/10.1186/1471-2164-14-501.
Töpfer, Armin, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, and Niko Beerenwinkel. 2014. “Viral Quasispecies Assembly via Maximal Clique Enumeration.” Edited by Alice Carolyn McHardy. PLoS Computational Biology 10 (3): e1003515. https://doi.org/10.1371/journal.pcbi.1003515.
Zagordi, Osvaldo, Arnab Bhattacharya, Nicholas Eriksson, and Niko Beerenwinkel. 2011. “ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.” BMC Bioinformatics 12 (1): 119. https://doi.org/10.1186/1471-2105-12-119.
Zagordi, Osvaldo, Lukas Geyrhofer, Volker Roth, and Niko Beerenwinkel. 2010. “Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.” J. Comput. Biol. 17 (3): 417–28. https://doi.org/10.1089/cmb.2009.0164.
Zagordi, Osvaldo, Rolf Klein, Martin Däumer, and Niko Beerenwinkel. 2010. “Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.” Nucleic Acids Research 38 (21): 7400–7409. https://doi.org/10.1093/nar/gkq655.