ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies

Background SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVI...

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Published in:BMC bioinformatics Vol. 23; no. 1; pp. 196 - 16
Main Authors: Plyusnin, Ilya, Truong Nguyen, Phuoc Thien, Sironen, Tarja, Vapalahti, Olli, Smura, Teemu, Kant, Ravi
Format: Journal Article
Language:English
Published: London BioMed Central 28.05.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Analysis
Bioinformatics
Biomedical and Life Sciences
Cladistic analysis
Cluster analysis
Computational Biology
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Coronaviruses
Cost analysis
COVID-19
COVID-19 vaccines
DNA Viruses
Epidemics
Epidemiology
Etiology
Genetic aspects
Genomes
Health surveillance
Humans
Life Sciences
Methods
Microarrays
Mutation
Operating costs
Outliers (statistics)
Pandemics
Pathogens
Phylogenetic analysis
Phylogenetics
Phylogeny
Public health
SARS-CoV-2
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Software
Trees
Variant calling
Viral diseases
Virus
Viruses
Finland
Phylogenetic analysis
Cluster analysis
Virus
SARS-CoV-2
Variant calling
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:Background SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in-depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance. Results Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high-level functionalities including lineage assignment, outlier filtering, aligning, phylogenetic tree reconstruction, cluster extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland with the main emphasis on fast screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations. Conclusions ClusTRace provides an effective interface that can significantly cut down learning and operating costs related to complex bioinformatic analysis of large viral sequence sets and phylogenies. All code is freely available from https://bitbucket.org/plyusnin/clustrace/
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-022-04709-8