ArticleMicrobial genomics2025
Exploring SNP filtering strategies: the influence of strict vs soft core.
Article in Microbial genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Azithromycin-resistantJAC-antimicrobial resistance · 2026Article
- Pathogen genome enrichment sequencing to support a city-wide Legionnaires' disease outbreak investigation.Microbial genomics · 2026Article
- Buscogeny: A BUSCO leveraged phylogenomic tree builder.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle.PLOS global public health · 2026Article
- Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.PLoS pathogens · 2025Article
- Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.Current opinion in infectious diseases · 2025Review
- Conserved genome structure and phylogenetic insights for the heterogeneous subfamily of Convallarioideae (Asparagaceae) revealed from plastome data.BMC plant biology · 2025Article
- Article
- Comprehensive epidemiological profiling of poultry-derivedFrontiers in microbiology · 2025Article
- Artisanal food of animal origin as reservoir of putative pathogenicFrontiers in microbiology · 2025Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a 'strict core' by removing those sites that do not have data present in every sample. However, as sample size and genome diversity increase, a strict core can shrink markedly, discarding potentially informative data. Here, we propose and provide evidence to support the use of a 'soft core' that tolerates some missing data, preserving more information for phylogenetic analysis. Using large datasets of
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