ArticleNature communications2024
ContScout: sensitive detection and removal of contamination from annotated genomes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.Insect molecular biology · 2026Article
- Basidiomycete fruiting body morphology correlates with the convergent loss of photolyase-related proteins.iScience · 2026Article
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Structure-guided analysis of divergent homologs unveils deep ancestry and arthropod specialization of the pacifastin family.Scientific reports · 2026Article
- Contamination-Free Genome Assembly of Podosphaera xanthii Reveals Signatures of Obligate Biotrophy.The plant pathology journal · 2025Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.Genome research · 2025Article
- Small but Mitey: A Gapless Telomere-to-Telomere Assembly of an Unidentified Mite With a Streamlined Genome.Genome biology and evolution · 2025Article
- New insights into the charge property at active sites boost PMS activation over LaFeScientific reports · 2024Article
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Increased Evolutionary Rate in the Z chromosome of Sympatric and Allopatric Species of Morpho Butterflies.Genome biology and evolution · 2024Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi.G3 (Bethesda, Md.) · 2024Article
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7 authors.
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Abstract
Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.
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