ArticleNucleic acids research2015
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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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
91 citing papers in PubMed.
- Trial
- Article
- 16S rRNA sequence captures microbial functional potential.bioRxiv : the preprint server for biology · 2026Article
- Advances in pathogen detection ofInfectious medicine · 2025Review
- Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.BMC genomics · 2025Article
- Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.BMC microbiology · 2025Article
- Advancing metagenomic classification with NABAS+: a novel alignment-based approach.NAR genomics and bioinformatics · 2025Article
- Comprehensive Cross-Domain Taxonomic Classification of Microbiotas using Partitioned Amplification Multiplexed Amplicon Sequencing (PAMA-seq).bioRxiv : the preprint server for biology · 2025Article
- Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.mSystems · 2025Article
- Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.Computational and structural biotechnology journal · 2024Article
- Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection.Royal Society open science · 2024Article
- Genomic fingerprints of the world's soil ecosystems.mSystems · 2024Article
- Sea cucumber (Data in brief · 2024Article
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Combining compositional data sets introduces error in covariance network reconstruction.ISME communications · 2024Article
- Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.Viruses · 2023Review
- Leveraging microbiome rediversification for the ecological rescue of soil function.Environmental microbiome · 2023Article
- The IMG/M data management and analysis system v.7: content updates and new features.Nucleic acids research · 2023Article
- Article
- Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems.PloS one · 2023Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.
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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.