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

BMC Bioinformatics

Phuoc Thien Truong Nguyen¹  Ravi Kant²  Tarja Sironen²  Olli Vapalahti³  Teemu Smura⁴  Ilya Plyusnin⁵ 

[1] Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland;Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland;Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland;Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland;Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland;Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland;Institute of Biotechnology, University of Helsinki, Helsinki, Finland;Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland;

关键词: SARS-CoV2;    Variant detection;    Reference assembly;    Lineage identification;    Coronavirus;    Sequence analysis;   

DOI  :  10.1186/s12859-021-04294-2

来源: Springer

【 摘 要 】

BackgroundSARS-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.ResultsDue 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.ConclusionsHAVoC 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.

【 授权许可】

CC BY