ArticlemBio2025
Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.
Article in mBio, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- Magnetotaxis in an anaerobic ciliate via tripartite syntrophy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Review
- 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
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- From Permits to Samples: Addressing Key Challenges for High-Quality Reference Genome Generation in Europe.Molecular ecology resources · 2026Review
- A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.Scientific data · 2025Article
- The Role of Nucleotide Sequencing in Natural Product Drug Discovery.Journal of natural products · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for
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What OpenQuestion holds
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.