Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Identifieur interne : 002962 ( Main/Merge ); précédent : 002961; suivant : 002963Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Auteurs : Daniel R. Zerbino [Royaume-Uni] ; Ewan BirneySource :
- Genome research [ 1088-9051 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
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<term>Computer Simulation</term>
<term>Genome, Bacterial</term>
<term>Genome, Human</term>
<term>Genomics</term>
<term>Humans</term>
<term>Mammals (genetics)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Sequence Analysis, DNA (standards)</term>
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<term>Analyse de séquence d'ADN ()</term>
<term>Analyse de séquence d'ADN (normes)</term>
<term>Animaux</term>
<term>Biologie informatique ()</term>
<term>Chromosomes artificiels de bactérie</term>
<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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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mammals</term>
<term>Streptococcus</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Mammifères</term>
<term>Streptococcus</term>
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<term>Sequence Analysis, DNA</term>
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<term>Chromosomes, Artificial, Bacterial</term>
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<term>Analyse de séquence d'ADN</term>
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<term>Biologie informatique</term>
<term>Chromosomes artificiels de bactérie</term>
<term>Génome bactérien</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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