ArticlePLoS computational biology2021
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ClinicalFrontiers in microbiology · 2025Pooled it
- Scalable assembly of Ascaris mitogenomes from whole-genome data reveals a novel clade.Scientific reports · 2026Article
- Genomic epidemiology reveals geographically structured co-circulation of AFR10 and AFR13Microbial genomics · 2026Article
- A genome assembly of the North American golden eagle, Aquila chrysaetos canadensis.The Journal of heredity · 2026Article
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Two Australian genome assemblies expand the genomic blueprint of giant kelp.BMC genomics · 2026Article
- Complete genomes reveal a refined map of Mycobacterium tuberculosis genetic diversity across evolutionary scales.Nature communications · 2026Article
- Chromosome-level genome assembly of Xuefeng Black-bone chicken and comparative genomics analysis.BMC genomics · 2026Article
- Conspecific Scaffold-Level Genome Assembly Outperforms Heterospecific Chromosome-Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish.Evolutionary applications · 2026Article
- Using pangenome variation graphs to improve mutation detection in a large DNA virus.Microbial genomics · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Fifteen Years of the Genome Analysis Toolkit as the De Facto Standard in Short-Read Variant Calling.International journal of molecular sciences · 2026Review
- Low-level contamination confounds population genomic analysis.G3 (Bethesda, Md.) · 2026Article
- chewBBACA 3: lowering the barrier for scalable and detailed whole- and core-genome multilocus sequence typing.Genome medicine · 2026Article
- GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations.Heredity · 2026Article
- A genomic approach for accurate identification of closely related species with next-generation sequencing samples.Scientific reports · 2026Article
- Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae.bioRxiv : the preprint server for biology · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- Genomic Profiling and Mutation Analysis ofMicroorganisms · 2025Article
- Plasmid transmission dynamics and evolution of partner quality in a natural population ofmBio · 2025Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended.
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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.