MersV1, Main, Exploration, bibRecord, 002936

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Identifieur interne : 002936 ( Main/Exploration ); précédent : 002935; suivant : 002937

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Auteurs : Daniel R. Zerbino [Royaume-Uni] ; Ewan Birney

Source :

Genome research [ 1088-9051 ] ; 2008.

RBID : pubmed:18349386

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN (), Analyse de séquence d'ADN (normes), Animaux, Biologie informatique (), Chromosomes artificiels de bactérie, Génome bactérien, Génome humain, Génomique, Humains, Mammifères (génétique), Simulation numérique, Streptococcus (génétique).
MESH :
- génétique : Mammifères, Streptococcus.
- normes : Analyse de séquence d'ADN.
- Algorithmes, Analyse de séquence d'ADN, Animaux, Biologie informatique, Chromosomes artificiels de bactérie, Génome bactérien, Génome humain, Génomique, Humains, Simulation numérique.

English descriptors

KwdEn :
- Algorithms, Animals, Chromosomes, Artificial, Bacterial, Computational Biology (methods), Computer Simulation, Genome, Bacterial, Genome, Human, Genomics, Humans, Mammals (genetics), Sequence Analysis, DNA (methods), Sequence Analysis, DNA (standards), Streptococcus (genetics).
MESH :
- genetics : Mammals, Streptococcus.
- methods : Computational Biology, Sequence Analysis, DNA.
- standards : Sequence Analysis, DNA.
- Algorithms, Animals, Chromosomes, Artificial, Bacterial, Computer Simulation, Genome, Bacterial, Genome, Human, Genomics, Humans.

Abstract

We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.

DOI: 10.1101/gr.074492.107
PubMed: 18349386

Affiliations:

Royaume-Uni

Le document en format XML

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<term>Computer Simulation</term>
<term>Genome, Bacterial</term>
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<term>Biologie informatique ()</term>
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<term>Génome bactérien</term>
<term>Génome humain</term>
<term>Génomique</term>
<term>Humains</term>
<term>Mammifères (génétique)</term>
<term>Simulation numérique</term>
<term>Streptococcus (génétique)</term>
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<term>Streptococcus</term>
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<term>Streptococcus</term>
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<term>Sequence Analysis, DNA</term>
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<term>Chromosomes artificiels de bactérie</term>
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<term>Génomique</term>
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<front><div type="abstract" xml:lang="en">We have developed a new set of algorithms, collectively called "Velvet," to manipulate de Bruijn graphs for genomic sequence assembly. A de Bruijn graph is a compact representation based on short words (k-mers) that is ideal for high coverage, very short read (25-50 bp) data sets. Applying Velvet to very short reads and paired-ends information only, one can produce contigs of significant length, up to 50-kb N50 length in simulations of prokaryotic data and 3-kb N50 on simulated mammalian BACs. When applied to real Solexa data sets without read pairs, Velvet generated contigs of approximately 8 kb in a prokaryote and 2 kb in a mammalian BAC, in close agreement with our simulated results without read-pair information. Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies.</div>
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Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
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