ArticleMicrobial genomics2022
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.
Article in Microbial genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Comprehensive Evaluation of Safety and Probiotic Potential of Lactiplantibacillus plantarum HY7715 Isolated from Korean kimchi.Probiotics and antimicrobial proteins · 2026Article
- Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing.Microbial genomics · 2026Article
- Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.Scientific reports · 2026Article
- Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.Environmental microbiology reports · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- Detection ofFood chemistry. Molecular sciences · 2025Article
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- Optimization of 16S RNA Sequencing and Evaluation of Metagenomic Analysis with Kraken 2 and KrakenUniq.Diagnostics (Basel, Switzerland) · 2025Article
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.Virology journal · 2025Article
- PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.GigaScience · 2025Article
- RpNGS: an automated platform for pathogen identification and monitoring in clinical metagenomics data.PeerJ · 2025Article
- Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2.aBIOTECH · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- An in-depth evaluation of metagenomic classifiers for soil microbiomes.Environmental microbiome · 2024Article
- Interpretation of vaginal metagenomic characteristics in different types of vaginitis.mSystems · 2024Article
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.Bioinformatics advances · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Culture-independent metagenomic detection of microbial species has the potential to provide rapid and precise real-time diagnostic results. However, it is potentially limited by sequencing and taxonomic classification errors. We use simulated and real-world data to benchmark rates of species misclassification using 100 reference genomes for each of the ten common bloodstream pathogens and six frequent blood-culture contaminants (
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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.