ReviewGenome biology2022
Contamination detection in genomic data: more is not enough.
Review in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed.
- ProbeST: a custom probe design pipeline for dual host-pathogen Spatial Transcriptomics.BMC genomics · 2026Article
- CSI-SSU: phylogenetic contamination screening of genomic datasets, demonstrated on The Protist 10,000 Genomes (P10K) Project.BMC genomics · 2026Article
- Low-level contamination confounds population genomic analysis.G3 (Bethesda, Md.) · 2026Article
- krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.Genome biology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Molecular Phylogeny of "Chemosensory Proteins" in Bacteria and Arthropods: CSP as an Extremely Ancient Gene.Journal of molecular evolution · 2026Article
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
- Impact of sequencing read quality on whole-genome sequencing outcomes for foodborne pathogens using a BacWORK standardized analysis workflow.Bioinformatics advances · 2026Article
- Probiogenomics as a Computational Biotechnology Framework: Safety-Gated Genome Analytics for Candidate Probiotic Prioritization and Validation.Computational and structural biotechnology journal · 2026Review
- Making genomic data FAIR through effective Data Portals.Scientific data · 2025Article
- 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
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Review
- AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis.PLoS computational biology · 2025Article
- Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.GigaScience · 2025Article
- Quality assessment of gene repertoire annotations with OMArk.Nature biotechnology · 2025Article
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
The decreasing cost of sequencing and concomitant augmentation of publicly available genomes have created an acute need for automated software to assess genomic contamination. During the last 6 years, 18 programs have been published, each with its own strengths and weaknesses. Deciding which tools to use becomes more and more difficult without an understanding of the underlying algorithms. We review these programs, benchmarking six of them, and present their main operating principles. This article is intended to guide researchers in the selection of appropriate tools for specific applications. Finally, we present future challenges in the developing field of contamination detection.
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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.