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

Autor:	Truong Nguyen, Phuoc Thien, Plyusnin, Ilya, Sironen, Tarja, Vapalahti, Olli, Kant, Ravi, Smura, Teemu
Přispěvatelé:	Department of Virology, Medicum, Viral Zoonosis Research Unit, HUSLAB, Institute of Biotechnology, Veterinary Biosciences, Helsinki One Health (HOH), Emerging Infections Research Group, Veterinary Microbiology and Epidemiology, Olli Pekka Vapalahti / Principal Investigator
Jazyk:	angličtina
Předmět:	11832 Microbiology and virology Consensus Variant detection SARS-CoV-2 QH301-705.5 viruses Computer applications to medicine. Medical informatics fungi R858-859.7 Sequence analysis COVID-19 Computational Biology Reference assembly DISEASE body regions Coronavirus ALIGNMENT Lineage identification SARS-CoV2 Humans 3111 Biomedicine Biology (General) skin and connective tissue diseases Software Brazil
Zdroj:	BMC Bioinformatics, Vol 22, Iss 1, Pp 1-8 (2021) BMC Bioinformatics
ISSN:	1471-2105
DOI:	10.1186/s12859-021-04294-2
Popis:	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.
Databáze:	OpenAIRE
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