These are the primary publications about V-pipe itself.
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.
To cite V-pipe in a publication when you use the workflow for your analysis, please cite the most recent primary publication.
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.
Publications from our group members or collaborators in which V-pipe has been used to analyse NGS viral data.
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.
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.
Benchmark comparing the performance of V-pipe against other similar workflows.
Sutcliffe, Steven G., Susanne A. Kraemer, Isaac Ellmen, Jennifer J.
Knapp, Alyssa K. Overton, Delaney Nash, Jozef I. Nissimov, et al. 2023.
“Tracking SARS-CoV-2 Variants of Concern in Wastewater: An
Assessment of Nine Computational Tools Using Simulated Genomic
Data.” bioRxiv.
https://doi.org/10.1101/2023.12.20.572426.