ArticleGenome biology2020
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
150 citing papers in PubMed.
- Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.Gut microbes · 2026Review
- Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions.bioRxiv : the preprint server for biology · 2026Article
- Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.American journal of biological anthropology · 2026Article
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.Journal of clinical microbiology · 2026Article
- Distribution of poly(A) polymerase I in bacteria: an expanded role for horizontal gene transfer.Microbiology (Reading, England) · 2026Article
- Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review.World journal of microbiology & biotechnology · 2026Review
- DNA signatures preserved in the official 1978 sample collection of the Shroud of Turin.Scientific reports · 2026Article
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.bioRxiv : the preprint server for biology · 2026Article
- Article
- Systematic detection of Oxford Nanopore adapter and barcode contamination in GenBank.BMC genomics · 2026Article
- DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.BMC bioinformatics · 2026Article
- MitoNGS: an online platform to analyze fish metabarcoding data in high resolution.Molecular biology and evolution · 2026Article
- Article
- Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.BMC genomics · 2026Article
- Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.Evolutionary applications · 2026Article
- Planning and Analyzing a Low-Biomass Microbiome Study: A Data Analysis Perspective.The Journal of infectious diseases · 2026Review
- Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.Scientific reports · 2026Article
- Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.Frontiers in physiology · 2026Review
90 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
Genomic analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences. Here, we describe Conterminator, an efficient method to detect and remove incorrectly labeled sequences by an exhaustive all-against-all sequence comparison. Our analysis reports contamination of 2,161,746, 114,035, and 14,148 sequences in the RefSeq, GenBank, and NR databases, respectively, spanning the whole range from draft to "complete" model organism genomes. Our method scales linearly with input size and can process 3.3 TB in 12 days on a 32-core computer. Conterminator can help ensure the quality of reference databases. Source code (GPLv3): https://github.com/martin-steinegger/conterminator.
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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.