V-pipe

V-pipe analyzes NGS data from intra-host viral populations to generate high-quality read alignments, call low-frequency single-nucleotide variants, and infer viral haplotypes for studies of genetic diversity, transmission, and genomic surveillance.

Key Features:

Quality Control and Read Mapping: Integrates quality control and read mapping for NGS reads using configurable aligners and statistical models.
ngshmmalign (Novel Alignment Methodology): Implements profile hidden Markov models tailored to small, highly diverse viral genomes to improve alignment quality.
Low-Frequency Mutation Calling and Haplotype Inference: Detects low-frequency mutations and performs viral haplotype inference to characterize intra-host genetic diversity.
Benchmarking Functionality: Provides a standardized benchmarking environment to compare read aligners (Bowtie 2, BWA MEM, ngshmmalign) and variant callers (LoFreq, ShoRAH) for single-nucleotide variant calling performance.
Modular Implementation: Uses a modular architecture that enables substitution and configuration of pipeline components and benchmarking setups.

Scientific Applications:

Genomic Surveillance: Analyzes whole genome sequences to monitor variants such as SARS-CoV-2 B.1.1.7 and to estimate transmission fitness advantages and effective reproductive numbers.
One-Health Context Studies: Supports investigation of zoonotic transmissions, including SARS-CoV-2 infections in domestic cats.
Quantifying Genetic Diversity: Measures within-host genetic diversity to inform studies of disease progression, treatment outcomes, drug resistance, cell tropism, and transmission risks.

Methodology:

Performs quality control and read mapping; uses ngshmmalign (profile hidden Markov models) and supports Bowtie 2 and BWA MEM; applies variant callers LoFreq and ShoRAH; conducts haplotype inference and benchmarking of configurations.

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Topics

Genomics Population genetics Workflows Virology Sequencing

Collections

COVID-19

Details

License:: Apache-2.0
Maturity:: Mature
Cost:: Free of charge
Tool Type:: command-line tool, workflow
Operating Systems:: Linux, Mac
Programming Languages:: Shell, Python
Added:: 2/2/2018
Last Updated:: 11/24/2024

Operations

Publications

Carlisle LA, Turk T, Kusejko K, Metzner KJ, Leemann C, Schenkel CD, Bachmann N, Posada S, Beerenwinkel N, Böni J, Yerly S, Klimkait T, Perreau M, Braun DL, Rauch A, Calmy A, Cavassini M, Battegay M, Vernazza P, Bernasconi E, Günthard HF, Kouyos RD, Anagnostopoulos A, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Ledergerber B, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Rudin C, Scherrer AU, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Wandeler G, Weber R, Yerly S. 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. 2019;220(2):254-265. doi:10.1093/infdis/jiz094. PMID:30835266.

DOI: 10.1093/infdis/jiz094

PMID: 30835266

Funding: - Swiss National Science Foundation: 148522, 179571, BSSGI0_155851

Posada-Céspedes S, Seifert D, Topolsky I, Jablonski KP, Metzner KJ, Beerenwinkel N. V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinformatics. 2021;37(12):1673-1680. doi:10.1093/bioinformatics/btab015. PMID:33471068. PMCID:PMC8289377.

DOI: 10.1093/bioinformatics/btab015

PMID: 33471068

PMCID: PMC8289377

Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild A, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki E, O'Toole ÁN, Palacios-Ontiveros N, Petrov AI, Rangel-Piñeros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research. Unknown Journal. 2020. doi:10.20944/preprints202005.0376.v1.

DOI: 10.20944/preprints202005.0376.v1

Posada-Cespedes S, Seifert D, Beerenwinkel N. Recent advances in inferring viral diversity from high-throughput sequencing data. Virus Research. 2017;239:17-32. doi:10.1016/j.virusres.2016.09.016. PMID:27693290.

DOI: 10.1016/j.virusres.2016.09.016

PMID: 27693290

Ibrahim B, Arkhipova K, Andeweg A, Posada-Céspedes S, Enault F, Gruber A, Koonin E, Kupczok A, Lemey P, McHardy A, McMahon D, Pickett B, Robertson D, Scheuermann R, Zhernakova A, Zwart M, Schönhuth A, Dutilh B, Marz M. Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting. Viruses. 2018;10(5):256. doi:10.3390/v10050256. PMID:29757994. PMCID:PMC5977249.

DOI: 10.3390/v10050256

PMID: 29757994

PMCID: PMC5977249

Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O’Toole Á, Pereyaslov D. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance. 2020;25(32). doi:10.2807/1560-7917.es.2020.25.32.2001410. PMID:32794443. PMCID:PMC7427299.

DOI: 10.2807/1560-7917.es.2020.25.32.2001410

PMID: 32794443

PMCID: PMC7427299

Kuipers J, Batavia AA, Jablonski KP, Bayer F, Borgsmüller N, Dondi A, Drăgan M, Ferreira P, Jahn K, Lamberti L, Pirkl M, Posada-Céspedes S, Topolsky I, Nissen I, Santacroce N, Burcklen E, Schär T, Capece V, Beckmann C, Kobel O, Noppen C, Redondo M, Nadeau S, Seidel S, Santamaria de Souza N, Beisel C, Stadler T, Beerenwinkel N. Within-patient genetic diversity of SARS-CoV-2. Unknown Journal. 2020. doi:10.1101/2020.10.12.335919.

DOI: 10.1101/2020.10.12.335919

Nadeau S, Beckmann C, Topolsky I, Vaughan T, Hodcroft E, Schär T, Nissen I, Santacroce N, Burcklen E, Ferreira P, Jablonski KP, Posada-Céspedes S, Capece V, Seidel S, de Souza NS, Martinez-Gomez JM, Cheng P, Bosshard PP, Levesque MP, Kufner V, Schmutz S, Zaheri M, Huber M, Trkola A, Cordey S, Laubscher F, Gonçalves AR, Leuzinger K, Stange M, Mari A, Roloff T, Seth-Smith H, Hirsch HH, Egli A, Redondo M, Kobel O, Noppen C, Beerenwinkel N, Neher RA, Beisel C, Stadler T. Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data. Unknown Journal. 2020. doi:10.1101/2020.10.14.20212621.

DOI: 10.1101/2020.10.14.20212621

Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Detection and surveillance of SARS-CoV-2 genomic variants in wastewater. Unknown Journal. 2021. doi:10.1101/2021.01.08.21249379.

DOI: 10.1101/2021.01.08.21249379

Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Epidemics. 2021;37:100480. doi:10.1016/j.epidem.2021.100480. PMID:34488035. PMCID:PMC8452947.

DOI: 10.1016/j.epidem.2021.100480

PMID: 34488035

PMCID: PMC8452947

Klaus J, Meli M, Willi B, Nadeau S, Beisel C, Stadler T, Egberink H, Zhao S, Lutz H, Riond B, Rösinger N, Stalder H, Renzullo S, Hofmann-Lehmann R. Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland. Viruses. 2021;13(3):496. doi:10.3390/v13030496. PMID:33802899. PMCID:PMC8002591.

DOI: 10.3390/v13030496

PMID: 33802899

PMCID: PMC8002591

Funding: - Universität Zürich: G-53420-01-01 - Bundesamt für Lebensmittelsicherheit und Veterinärwesen: 0714001572, 0714001626

Fuhrmann L, Jablonski KP, Beerenwinkel N. Quantitative measures of within-host viral genetic diversity. Current Opinion in Virology. 2021;49:157-163. doi:10.1016/j.coviro.2021.06.002. PMID:34153841.

DOI: 10.1016/j.coviro.2021.06.002

PMID: 34153841

Funding: - Horizon 2020 Marie Skłodowska-Curie Actions: 955974