Primary

Posada-Céspedes, Susana, David Seifert, Ivan Topolsky, Karin J Metzner, and Niko Beerenwinkel. 2020. “V-Pipe: A Computational Pipeline for Assessing Viral Genetic Diversity from High-Throughput Sequencing Data.” bioRxiv. https://doi.org/10.1101/2020.06.09.142919.

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

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.

Components of V-pipe developed at CBG-ETHZ

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.