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HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

View ORCID ProfilePhuoc Truong Nguyen, View ORCID ProfileIlya Plyusnin, View ORCID ProfileTarja Sironen, View ORCID ProfileOlli Vapalahti, View ORCID ProfileRavi Kant, View ORCID ProfileTeemu Smura
doi: https://doi.org/10.1101/2021.02.12.431018
Phuoc Truong Nguyen
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Ilya Plyusnin
2Institute of Biotechnology, University of Helsinki, Helsinki, Finland
3Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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Tarja Sironen
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
3Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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Olli Vapalahti
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
3Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
4Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Ravi Kant
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
3Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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  • For correspondence: Ravi.Kant@helsinki.fi Teemu.Smura@helsinki.fi
Teemu Smura
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
4Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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  • For correspondence: Ravi.Kant@helsinki.fi Teemu.Smura@helsinki.fi
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Abstract

Background SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK variant B.1.1.7, the South African variant B1.351 and the Brazilian variant P.1. Detecting and monitoring novel variants is essential in SARS-CoV-2 surveillance. While there are several tools for assembling virus genomes and performing lineage analyses to investigate SARS-CoV-2, each is limited to performing singular or a few functions separately.

Results Due to the lack of publicly available pipelines, which could perform fast reference-based assemblies on raw SARS-CoV-2 sequences in addition to identifying lineages to detect variants of concern, we have developed an open source bioinformatic pipeline called HaVoC (Helsinki university Analyzer for Variants Of Concern). HaVoC can reference assemble raw sequence reads and assign the corresponding lineages to SARS-CoV-2 sequences.

Conclusions HaVoC is a pipeline utilizing several bioinformatic tools to perform multiple necessary analyses for investigating genetic variance among SARS-CoV-2 samples. The pipeline is particularly useful for those who need a more accessible and fast tool to detect and monitor the spread of SARS-CoV-2 variants of concern during local outbreaks. HaVoC is currently being used in Finland for monitoring the spread of SARS-CoV-2 variants. HaVoC user manual and source code are available at https://www.helsinki.fi/en/projects/havoc and https://bitbucket.org/auto_cov_pipeline/havoc, respectively.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://bitbucket.org/auto_cov_pipeline/havoc

  • List of abbreviations

    SARS-CoV-2
    Severe acute respiratory syndrome coronavirus 2
    COVID-19
    Coronavirus disease 2019
    HaVoC
    Helsinki university Analyzer for Variants Of Concern
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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    HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
    Phuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura
    bioRxiv 2021.02.12.431018; doi: https://doi.org/10.1101/2021.02.12.431018
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    HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences
    Phuoc Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant, Teemu Smura
    bioRxiv 2021.02.12.431018; doi: https://doi.org/10.1101/2021.02.12.431018

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