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HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2
Phuoc Thien Truong Nguyen1, Ilya Plyusnin2,3, Tarja Sironen4,3
1Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. phuoc.truong@helsinki.fi.
BMC Bioinformatics
|July 18, 2021
Summary
A new open-source pipeline, HAVoC, enables rapid detection and monitoring of SARS-CoV-2 variants of concern. This tool aids global surveillance efforts by analyzing genetic variance in virus samples.
Area of Science:
- Virology
- Bioinformatics
- Genomic Surveillance
Background:
- The emergence of SARS-CoV-2 variants (e.g., B.1.1.7, B.1.351, P.1) necessitates robust global surveillance.
- Existing tools for SARS-CoV-2 genome analysis are often limited to single functions, hindering comprehensive variant detection.
Purpose of the Study:
- To develop an integrated, open-source bioinformatic pipeline for rapid SARS-CoV-2 variant analysis.
- To address the need for a tool that combines reference-based assembly and lineage identification for variants of concern.
Main Methods:
- Development of the HAVoC (Helsinki university Analyzer for Variants of Concern) pipeline.
- Integration of multiple bioinformatic tools for comprehensive analysis of SARS-CoV-2 sequences.
Main Results:
- HAVoC performs reference-based assembly of raw SARS-CoV-2 sequence reads.
- The pipeline accurately assigns lineages, facilitating the identification of variants of concern.
Conclusions:
- HAVoC provides an accessible and fast solution for investigating SARS-CoV-2 genetic variance.
- The pipeline is crucial for monitoring the spread of SARS-CoV-2 variants during local outbreaks.
- HAVoC is actively used in Finland for SARS-CoV-2 variant surveillance.
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