ArticleGenome biology2021
STRONG: metagenomics strain resolution on assembly graphs.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 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
70 citing papers in PubMed.
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- SNooPy: a statistical framework for long-read metagenomic variant calling.Nucleic acids research · 2026Article
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- High-quality metagenome assembly from nanopore reads with nanoMDBG.Nature communications · 2026Article
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?Frontiers in microbiology · 2026Article
- Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.Molecular ecology · 2025Article
- Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.Genomics, proteomics & bioinformatics · 2025Review
- Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.Cell genomics · 2025Article
- A Graph Contrastive Learning Method for Enhancing Genome Recovery in Complex Microbial Communities.Entropy (Basel, Switzerland) · 2025Article
- Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.Nature microbiology · 2025Article
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Article
- Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.The ISME journal · 2025Article
- ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.Frontiers in microbiology · 2025Article
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
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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.