ArticleNature biotechnology2018
High-quality genome sequences of uncultured microbes by assembly of read clouds.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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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.
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Who cites it
56 citing papers in PubMed.
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.mSystems · 2025Article
- Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.Nature communications · 2024Article
- Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.Microbiology spectrum · 2024Article
- LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.GigaScience · 2024Article
- Article
- Microbiome single cell atlases generated with a commercial instrument.Research square · 2023Article
- High-resolution single-molecule long-fragment rRNA gene amplicon sequencing of bacterial and eukaryotic microbial communities.Cell reports methods · 2023Article
- Whole-genome sequencing reveals high-risk clones ofFrontiers in microbiology · 2023Article
- Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.Frontiers in bioinformatics · 2023Review
- Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.Frontiers in microbiology · 2023Article
- MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads.iMeta · 2022Article
- VeChat: correcting errors in long reads using variation graphs.Nature communications · 2022Article
- Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.Microbiome · 2022Article
- Efficient detection and assembly of non-reference DNA sequences with synthetic long reads.Nucleic acids research · 2022Article
- Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.Nature communications · 2022Article
- Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults.Nature communications · 2022Article
- Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes.Molecular biology and evolution · 2022Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (>200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (>70% complete, <10% contaminated), nine of which were complete (>90% complete, <5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.
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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.