ArticleGenome biology2017
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 185 papers, 1 of them a synthesis that pooled it.
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Who cites it
185 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.Heart failure reviews · 2022Pooled it
- Gut microbiome stability and dynamics in healthy donors and patients with non-gastrointestinal cancers.The Journal of experimental medicine · 2021Trial
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.Virology journal · 2026Article
- Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.BMC microbiology · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.BMC oral health · 2026Observational
- Towards standardization in pig microbiome research based on a comprehensive twenty-year review.Animal microbiome · 2026Review
- Evaluating the analytical performance of direct-to-consumer gut microbiome testing services.Communications biology · 2026Article
- Filtering for truth: high-precision taxonomic classification in nanopore shotgun metagenomics data through a KMA-based bioinformatic pipeline (KAPTAIN).BMC genomics · 2026Article
- Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.BMC microbiology · 2026Article
- Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.PLoS computational biology · 2026Article
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial 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
- Hybrid expert system for robust detection of rare sequence signals: a computational proof-of-concept in host-dominated backgrounds.Frontiers in microbiology · 2026Article
- Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.Journal of virology · 2025Review
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
125 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
20 authors.
Funding
Abstract
backgroundOne of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.
resultsIn this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers. Tools were characterized on the basis of their ability to identify taxa at the genus, species, and strain levels, quantify relative abundances of taxa, and classify individual reads to the species level. Strikingly, the number of species identified by the 11 tools can differ by over three orders of magnitude on the same datasets. Various strategies can ameliorate taxonomic misclassification, including abundance filtering, ensemble approaches, and tool intersection. Nevertheless, these strategies were often insufficient to completely eliminate false positives from environmental samples, which are especially important where they concern medically relevant species. Overall, pairing tools with different classification strategies (k-mer, alignment, marker) can combine their respective advantages.
conclusionsThis study provides positive and negative controls, titrated standards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, accuracy, and recall. We show that proper experimental design and analysis parameters can reduce false positives, provide greater resolution of species in complex metagenomic samples, and improve the interpretation of results.
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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.