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Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4266. [Epub ahead of print]

High-quality genome sequences of uncultured microbes by assembly of read clouds.

Author information

1
Department of Computer Science, Stanford University, Stanford, California, USA.
2
Department of Medicine (Hematology, Blood and Marrow Transplantation) and Department of Genetics, Stanford University, Stanford, California, USA.
3
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
4
Department of Earth System Science, Stanford University, Stanford, California, USA.
5
Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.

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.

PMID:
30320765
DOI:
10.1038/nbt.4266

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