ArticleScientific reports2016
An evaluation of the accuracy and speed of metagenome analysis tools.
Article in Scientific reports, 2016. 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 170 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
170 citing papers in PubMed.
- Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.Briefings in bioinformatics · 2026Article
- Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.Nature communications · 2026Article
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 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
- Metagenomic Assembly and Gene Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.Molecular genetics and genomics : MGG · 2025Article
- Impact of Parenteral Ceftiofur on Developmental Dynamics of Early Life Fecal Microbiota and Antibiotic Resistome in Neonatal Lambs.Antibiotics (Basel, Switzerland) · 2025Article
- Diversified Soil Types Differentially Regulated the Peanut (Plants (Basel, Switzerland) · 2025Article
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.Microbial genomics · 2025Article
- MetaComBin: combining abundances and overlaps for binning metagenomics reads.Frontiers in bioinformatics · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Article
- Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.BMC research notes · 2024Article
- Taxanorm: a novel taxa-specific normalization approach for microbiome data.BMC bioinformatics · 2024Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- CAIM: coverage-based analysis for identification of microbiome.Briefings in bioinformatics · 2024Article
- CAIM: Coverage-based Analysis for Identification of Microbiome.bioRxiv : the preprint server for biology · 2024Article
- Meta-omics assisted microbial gene and strain resources mining in contaminant environment.Engineering in life sciences · 2024Review
- An in-depth evaluation of metagenomic classifiers for soil microbiomes.Environmental microbiome · 2024Article
110 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenome studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial and aquatic ecosystems to human skin and gut. With the advent of high-throughput sequencing platforms, the use of large scale shotgun sequencing approaches is now commonplace. However, a thorough independent benchmark comparing state-of-the-art metagenome analysis tools is lacking. Here, we present a benchmark where the most widely used tools are tested on complex, realistic data sets. Our results clearly show that the most widely used tools are not necessarily the most accurate, that the most accurate tool is not necessarily the most time consuming, and that there is a high degree of variability between available tools. These findings are important as the conclusions of any metagenomics study are affected by errors in the predicted community composition and functional capacity. Data sets and results are freely available from http://www.ucbioinformatics.org/metabenchmark.html.
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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.