ArticleNature communications2025
Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Article
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- VirBinn improves viral genome binning from metagenomic Hi-C through graph diffusion.Bioinformatics (Oxford, England) · 2026Article
- Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.Nature communications · 2026Article
- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.World journal of microbiology & biotechnology · 2026Article
- Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.Animal microbiome · 2026Article
- Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.Nature communications · 2026Article
- End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.bioRxiv : the preprint server for biology · 2026Article
- Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.Research square · 2026Article
- Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.Scientific data · 2026Article
- Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Metagenomic binning is a culture-free approach that facilitates the recovery of metagenome-assembled genomes by grouping genomic fragments. However, there remains a lack of a comprehensive benchmark to evaluate the performance of metagenomic binning tools across various combinations of data types and binning modes. In this study, we benchmark 13 metagenomic binning tools using short-read, long-read, and hybrid data under co-assembly, single-sample, and multi-sample binning, respectively. The benchmark results demonstrate that multi-sample binning exhibits optimal performance across short-read, long-read, and hybrid data. Moreover, multi-sample binning outperforms other binning modes in identifying potential antibiotic resistance gene hosts and near-complete strains containing potential biosynthetic gene clusters across diverse data types. This study also recommends three efficient binners across all data-binning combinations, as well as high-performance binners for each combination.
Indexed as
Identifiers
What OpenQuestion holds
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.