ArticleFrontiers in microbiology2021
Contamination in Reference Sequence Databases: Time for Divide-and-Rule Tactics.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Phylogenomic and Comparative Genomic Analyses Reveal Deep Evolutionary Structure and Cryptic Diversity in the GenusInternational journal of molecular sciences · 2026Article
- Reply to: Genome contamination may lead to an overestimation of horizontal gene transfer inferences.Nature communications · 2026Article
- Two novel real-time PCR assays forMicrobiology spectrum · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Article
- Identification and characterization of archaeal pseudomurein biosynthesis genes through pangenomics.mSystems · 2025Article
- Article
- Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.GigaScience · 2025Article
- Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.Frontiers in microbiology · 2025Article
- Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.Briefings in bioinformatics · 2024Article
- β-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).BMC plant biology · 2024Article
- In silico analyses identify sequence contamination thresholds for Nanopore-generated SARS-CoV-2 sequences.PLoS computational biology · 2024Article
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.Genome biology · 2024Article
- ContScout: sensitive detection and removal of contamination from annotated genomes.Nature communications · 2024Article
- GTax: improving de novo transcriptome assembly by removing foreign RNA contamination.Genome biology · 2024Article
- Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG.F1000Research · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.Scientific reports · 2023Article
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Contaminating sequences in public genome databases is a pervasive issue with potentially far-reaching consequences. This problem has attracted much attention in the recent literature and many different tools are now available to detect contaminants. Although these methods are based on diverse algorithms that can sometimes produce widely different estimates of the contamination level, the majority of genomic studies rely on a single method of detection, which represents a risk of systematic error. In this work, we used two orthogonal methods to assess the level of contamination among National Center for Biotechnological Information Reference Sequence Database (RefSeq) bacterial genomes. First, we applied the most popular solution, CheckM, which is based on gene markers. We then complemented this approach by a genome-wide method, termed Physeter, which now implements a
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