ArticleFrontiers in genetics2022
Enhancing Long-Read-Based Strain-Aware Metagenome Assembly.
Article in Frontiers in genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- A Systems Approach to Endophyte-Mediated Plant Holobiont and Microbiome Dynamics.Plants (Basel, Switzerland) · 2026Review
- MADRe: Strain-level metagenomic classification through assembly-driven database reduction.GigaScience · 2026Article
- Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.Microbiology spectrum · 2025Article
- Repeat and haplotype aware error correction in nanopore sequencing reads with DeChat.Communications biology · 2024Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- Article
- Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-ProducingMicroorganisms · 2023Article
- VeChat: correcting errors in long reads using variation graphs.Nature communications · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art
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Registered trials
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