ArticleGigaScience2020
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 141 citations in OpenAlex.
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- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Deciphering the genomic landscape of hypervirulent Klebsiella pneumoniae in South African tertiary hospitals.BMC microbiology · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Assessing Amplification Quality and Bias in MDA Methods Through Comparative Analysis of Short-Read Sequencing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Genomic pitfalls in hospital surveillance: unexpected Enterobacter cloacae clustering without epidemiological link highlights the need for cautious core genome MLST analysis interpretation.Antimicrobial resistance and infection control · 2025Article
- High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.Current opinion in infectious diseases · 2025Review
- How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens.Microbial genomics · 2025Article
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Beyond patient contact: combined short- and long read sequencing reveals continuous occurrence of genomically related carbapenemase-producing Enterobacterales and plasmid mobility in a hospital, Germany, 2018 to 2021.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- Intra-host genomic variation of serologically nontypeableMicrobiology spectrum · 2025Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundAccurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella.
resultsWe evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis.
conclusionsThe accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.