ArticleNature methods2020
metaFlye: scalable long-read metagenome assembly using repeat graphs.
Article in Nature methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 669 papers.
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Who cites it
669 citing papers in PubMed.
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- The planktonic microbiome of the Great Barrier Reef.Nature · 2026Article
- Genomic insights into the taxonomy, safety and biotechnological potential ofMicrobial genomics · 2026Article
- DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.Briefings in bioinformatics · 2026Article
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- BioTester: an AI-driven automated testing framework for identifying potential quality risks in bioinformatics software.Briefings in bioinformatics · 2026Article
- Nanopore metagenomic sequencing links clinically relevant resistance determinants to pathogens.Microbial genomics · 2026Article
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11 authors.
Funding
Abstract
Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.
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