ArticleMicrobial genomics2019
Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP.
Article in Microbial genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed.
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- Probing Genomic Diversity ofFoods (Basel, Switzerland) · 2026Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.bioRxiv : the preprint server for biology · 2025Article
- A foodborne outbreak caused by atypical enteropathogenicApplied and environmental microbiology · 2025Article
- One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings.The Journal of antimicrobial chemotherapy · 2025Article
- Combination therapy delays antimicrobial resistance after adaptive laboratory evolution ofAntimicrobial agents and chemotherapy · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139Microbial genomics · 2025Article
- CFSAN SNP Pipeline 2 (CSP2): a pipeline for fast and accurate SNP distance estimation from bacterial genome assemblies.PeerJ. Computer science · 2025Article
- Article
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- Mobile genetic element-driven genomic changes in a community-associated methicillin-resistantMicrobial genomics · 2024Article
- Increased resistance against tellurite is conferred by a mutation in the promoter region of uncommon tellurite resistance geneApplied and environmental microbiology · 2024Article
- Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens.Journal of clinical microbiology · 2024Article
- Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157.Communications biology · 2024Article
- Combined usage of serodiagnosis and O antigen typing to isolate Shiga toxin-producingMicrobiology spectrum · 2024Article
- Atypical diarrhoeagenicEpidemiology and infection · 2023Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Bacteria are highly diverse, even within a species; thus, there have been many studies which classify a single species into multiple types and analyze the genetic differences between them. Recently, the use of whole-genome sequencing (WGS) has been popular for these analyses, and the identification of single-nucleotide polymorphisms (SNPs) between isolates is the most basic analysis performed following WGS. The performance of SNP-calling methods therefore has a significant effect on the accuracy of downstream analyses, such as phylogenetic tree inference. In particular, when closely related isolates are analyzed, e.g. in outbreak investigations, some SNP callers tend to detect a high number of false-positive SNPs compared with the limited number of true SNPs among isolates. However, the performances of various SNP callers in such a situation have not been validated sufficiently. Here, we show the results of realistic benchmarks of commonly used SNP callers, revealing that some of them exhibit markedly low accuracy when target isolates are closely related. As an alternative, we developed a novel pipeline BactSNP, which utilizes both assembly and mapping information and is capable of highly accurate and sensitive SNP calling in a single step. BactSNP is also able to call SNPs among isolates when the reference genome is a draft one or even when the user does not input the reference genome. BactSNP is available at https://github.com/IEkAdN/BactSNP.
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