About: An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

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About: An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
Creator	Li, Linlin Delwart, Eric Deng, Xutao Chiu, Charles Federman, Scot Ng, Terry Naccache, Samia
Source	Medline; PMC
abstract	Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.
has issue date	2015-04-20(xsd:dateTime)
bibo:doi	10.1093/nar/gkv002
bibo:pmid	25586223
has license	cc-by
sha1sum (hex)	8f11a3876dfbf3ba4a143b9e2ad122b8c2b9c2be
schema:url	https://doi.org/10.1093/nar/gkv002
resource representing a document's title	An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
has PubMed Central identifier	PMC4402509
has PubMed identifier	25586223
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:8f11a3876dfbf3ba4a143b9e2ad122b8c2b9c2be#body_text
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