ArticleVirus evolution2022
covSampler: A subsampling method with balanced genetic diversity for large-scale SARS-CoV-2 genome data sets.
Article in Virus evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Temporal dynamics of SARS-CoV-2 phylogenetic diversity in Central Brazil reveals evolutionary shifts among variants of concern during the pandemic.Frontiers in microbiology · 2025Article
- Recombinant SARS-CoV-2 Delta/Omicron BA.5 emerging in an immunocompromised long-term infected COVID-19 patient.Scientific reports · 2024Article
- The spatiotemporal analysis of SARS-CoV-2 transmission in China since the termination of the dynamic zero-COVID policy.Virologica Sinica · 2024Article
- Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.Viruses · 2023Review
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9 authors.
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Abstract
Phylogenetic analysis has been widely used to describe, display, and infer the evolutionary patterns of viruses. The unprecedented accumulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes has provided valuable materials for the real-time study of SARS-CoV-2 evolution. However, the large number of SARS-CoV-2 genome sequences also poses great challenges for data analysis. Several methods for subsampling these large data sets have been introduced. However, current methods mainly focus on the spatiotemporal distribution of genomes without considering their genetic diversity, which might lead to post-subsampling bias. In this study, a subsampling method named covSampler was developed for the subsampling of SARS-CoV-2 genomes with consideration of both their spatiotemporal distribution and their genetic diversity. First, covSampler clusters all genomes according to their spatiotemporal distribution and genetic variation into groups that we call divergent pathways. Then, based on these divergent pathways, two kinds of subsampling strategies, representative subsampling and comprehensive subsampling, were provided with adjustable parameters to meet different users' requirements. Our performance and validation tests indicate that covSampler is efficient and stable, with an abundance of options for user customization. Overall, our work has developed an easy-to-use tool and a webserver (https://www.covsampler.net) for the subsampling of SARS-CoV-2 genome sequences.
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