Exploring SNP Filtering Strategies: The Influence of Strict vs Soft Core

Abstract

ABSTRACTPhylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from single nucleotide polymorphism (SNP) alignments, with SNPs as the fundamental signal within these data. SNP alignments can be reduced to a ‘strict core’ containing only sites present in all samples. However, as sample size and genome diversity increase, a strict core can shrink markedly, resulting in lost 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 ofNeisseria gonorrhoeaeandSalmonella entericaserovar Typhi, we assess different core thresholds. Our results show that strict cores can drastically reduce informative sites compared to soft cores. In a 10,000-genome alignment ofS. Typhi, a 95% soft core yielded 10 times more informative sites than a 100% strict core. Similar patterns were observed inN. gonorrhoeae. We further evaluated the accuracy of phylogenies built from strict- and soft-core alignments using datasets with strong temporal signals. Soft-core alignments generally outperformed strict cores in producing trees that support clock-like behaviour; for instance, theN. gonorrhoeae95% soft-core phylogeny had a root-to-tip regressionR2of 0.50 compared to 0.21 for the strict-core phylogeny. This study suggests that soft-core strategies are preferable for large, diverse microbial datasets. To facilitate this, we developedCore-SNP-filter(github.com/rrwick/Core-SNP-filter), a tool for generating soft-core alignments based on user-defined thresholds.IMPACT STATEMENTThis study addresses a major limitation in modern microbial genomics – the significant data loss observed in large datasets for phylogenetic analyses, often due to strict-core SNP alignment approaches. As microbial genome sequence datasets grow and variation increases, a strict-core approach can greatly reduce the number of informative sites, compromising phylogenetic resolution. Our research highlights the advantages of soft-core alignment methods which tolerate some missing data and retain more genetic information. To streamline the processing of alignments, we developedCore-SNP-filter(github.com/rrwick/Core-SNP-filter), a publicly available resource-efficient tool that provides informative and core sites.DATA SUMMARYNo new reads were generated for this study. All reads used in this study are publicly available and accessions can be found in Supplementary Dataset 1. Supplementary methods and all code can be found in the accompanying GitHub repository: (github.com/mtaouk/Core-SNP-filter-methods).