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Reconstruction of B...
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes.
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Gupta, Ankit (författare)
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- Kumar, Sanjiv (författare)
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, United States
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Prasoodanan, Vishnu P. K. (författare)
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Harish, K. (författare)
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Sharma, Ashok K. (författare)
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Sharma, Vineet K. (författare)
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(creator_code:org_t)
- 2016-04-12
- 2016
- Engelska.
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Ingår i: Frontiers in Microbiology. - : Frontiers Media S.A.. - 1664-302X. ; 7:April
- Relaterad länk:
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https://www.frontier...
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https://urn.kb.se/re...
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https://doi.org/10.3...
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Abstract
Ämnesord
Stäng
- Several metagenomic projects have been accomplished or are in progress. However, in most cases, it is not feasible to generate complete genomic assemblies of species from the metagenomic sequencing of a complex environment. Only a few studies have reported the reconstruction of bacterial genomes from complex metagenomes. In this work, Binning-Assembly approach has been proposed and demonstrated for the reconstruction of bacterial and viral genomes from 72 human gut metagenomic datasets. A total 1156 bacterial genomes belonging to 219 bacterial families and, 279 viral genomes belonging to 84 viral families could be identified. More than 80% complete draft genome sequences could be reconstructed for a total of 126 bacterial and 11 viral genomes. Selected draft assembled genomes could be validated with 99.8% accuracy using their ORFs. The study provides useful information on the assembly expected for a species given its number of reads and abundance. This approach along with spiking was also demonstrated to be useful in improving the draft assembly of a bacterial genome. The Binning-Assembly approach can be successfully used to reconstruct bacterial and viral genomes from multiple metagenomic datasets obtained from similar environments.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Nyckelord
- bacterial draft genomes
- binning
- genome assembly
- metagenome
- spiking
- viral draft genomes
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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