ArticleGenome biology2020
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.
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 99 papers, 1 of them a synthesis that pooled it.
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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
99 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Primer-Less Species Identification Throughout Fungal (International journal of molecular sciences · 2026Article
- Gastrointestinal parasites of red and roe deer investigated via metagenomics and histology.Parasites & vectors · 2026Article
- 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
- Novel 20th century rotavirus alphagastroenteritidis strains identified in formalin-fixed and ethanol-preserved museum specimens.Molecular biology and evolution · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.Molecular ecology resources · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- A Novel Crustavirus as a Candidate Aetiology of Tail Fan Necrosis in New Zealand Red Rock Lobsters, Jasus edwardsii.Journal of fish diseases · 2026Article
- Impact of Silver Nanoparticles on the Gut Microbiota of the EarthwormInternational journal of molecular sciences · 2026Article
- From diversity to function: microbiome-mediated plant growth promotion, secondary metabolism, and antimicrobial resistance inFrontiers in bioinformatics · 2026Article
- Article
- Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.Inflammatory bowel diseases · 2025Article
- Multi-species eDNA as a screening tool to facilitate early detection and eradication of aquatic invasive species in large water bodies.Scientific reports · 2025Article
- Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA.NAR genomics and bioinformatics · 2025Article
- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Phylogenetic Diversity and Geographic Distribution of Atlantic Salmon Calicivirus in Major Salmon Farming Regions.Journal of fish diseases · 2025Article
- Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review.Food and waterborne parasitology · 2025Review
- Minimal disruption of equine gut microbiota by intravenous cephalothin treatment.The Journal of veterinary medical science · 2025Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to develop a highly accurate metagenomic classification pipeline named CCMetagen. The pipeline substantially outperforms other commonly used software in identifying bacteria and fungi and can efficiently use the entire NCBI nucleotide collection as a reference to detect species with incomplete genome data from all biological kingdoms. CCMetagen is user-friendly, and the results can be easily integrated into microbial community analysis software for streamlined and automated microbiome studies.
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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.