ArticleGenome biology2020
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC.
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 76 papers.
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Who cites it
76 citing papers in PubMed.
- A Simplified Guide to Whole-Genome Sequence Analysis of Salmonella on the Command Line.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Eukaryotic metagenome-assembled genomes recovered from deep metagenomic sequencing of the seagrass,Microbial genomics · 2026Article
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- Single-Thallus Genomics of Ejectosporus trisporus, an Unculturable Stonefly Gut Fungal Symbiont.Environmental microbiology · 2026Article
- De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics.Marine biotechnology (New York, N.Y.) · 2026Article
- Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.Nature communications · 2026Article
- Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.The Journal of investigative dermatology · 2026Article
- Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.Animal microbiome · 2026Article
- Ultra-deep metagenomic sequencing enables reconstruction of diverse, high quality microbial genomes from human urine samples.BMC microbiology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Phylogenomics of Plasmopara halstedii Reveals Genomic Regions Associated With the Breakdown of Sunflower Downy Mildew Resistance Genes.Molecular ecology · 2026Article
- Genome-resolved metagenomics reveals rare taxa and functional traits in two contrasting agricultural fields.ISME communications · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.PloS one · 2026Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- A genomic perspective on fungal diversity and evolution.Nature reviews. Microbiology · 2025Review
- Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.Microbiome · 2025Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
- Article
- Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.Cell host & microbe · 2025Article
16 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.
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