ArticlePloS one2016
Human Contamination in Public Genome Assemblies.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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.
The trial behind it
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
38 citing papers in PubMed.
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.mSystems · 2025Article
- Hybridization capture sequencing formBio · 2025Article
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.Genome biology · 2024Article
- A Large-Scale Study into Protist-Animal Interactions Based on Public Genomic Data Using DNA Barcodes.Animals : an open access journal from MDPI · 2023Article
- GenomeFLTR: filtering reads made easy.Nucleic acids research · 2023Article
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Rapid and sensitive detection of genome contamination at scale with FCS-GX.bioRxiv : the preprint server for biology · 2023Article
- Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.Cell reports methods · 2023Article
- Contamination detection in genomic data: more is not enough.Genome biology · 2022Review
- Beyond Nuclear Ribosomal DNA Sequences: Evolution, Taxonomy, and Closest Known Saprobic Relatives of Powdery Mildew Fungi (Frontiers in microbiology · 2022Article
- An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation.Retrovirology · 2021Article
- FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.Genes · 2021Article
- Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes.Scientific reports · 2021Article
- Article
- Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives.Frontiers in microbiology · 2021Review
- SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes.PLoS computational biology · 2020Article
- Evaluation of methods for detecting human reads in microbial sequencing datasets.Microbial genomics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. Although bacterial contamination is well known, the problem of human-originated contamination received little attention. In this study we surveyed 45,735 available genome assemblies for evidence of human contamination. We used lineage specificity to distinguish between contamination and conservation. We found that 154 genome assemblies contain fragments that with high confidence originate as contamination from human DNA. Majority of contaminating human sequences were present in the reference human genome assembly for over a decade. We recommend that existing contaminated genomes should be revised to remove contaminated sequence, and that new assemblies should be thoroughly checked for presence of human DNA before submitting them to public databases.
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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.