Primary

Fuhrmann, Lara, Kim Philipp Jablonski, Ivan Topolsky, Aashil A Batavia, Nico Borgsmueller, Pelin Icer Baykal, Matteo Carrara, et al. 2023. “V-Pipe 3.0: A Sustainable Pipeline for Within-Sample Viral Genetic Diversity Estimation.” bioRxiv. https://doi.org/10.1101/2023.10.16.562462.
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.
Lezcano, Oscar M., Lara Fuhrmann, Gayatri Ramakrishnan, Niko Beerenwinkel, Martijn A. Huynen, and Ronald P. van Rij. 2023. “Parallel Evolution and Enhanced Virulence Upon in Vivo Passage of an RNA Virus in Drosophila Melanogaster.” bioRxiv. https://doi.org/10.1101/2023.07.21.549997.
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.
Zhakparov, Damir, Yves Quirin, Yi Xiao, Nicole Battaglia, Michael Holzer, Martin Bühler, Walter Kistler, et al. 2023. “Sequencing of SARS-CoV-2 RNA Fragments in Wastewater Detects the Spread of New Variants During Major Events.” Microorganisms 11 (11). https://doi.org/10.3390/microorganisms11112660.

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.