OperaV1, Main, Exploration, bibRecord, 000A74

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Identifieur interne : 000A74 ( Main/Exploration ); précédent : 000A73; suivant : 000A75

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Auteurs : Song Gao [Singapour] ; Wing-Kin Sung ; Niranjan Nagarajan

Source :

Journal of computational biology : a journal of computational molecular cell biology ; 2011.

RBID : pubmed:21929371

English descriptors

KwdEn :
- Algorithms, Burkholderia pseudomallei (genetics), Computer Simulation, Contig Mapping (methods), Escherichia coli (genetics), Genome, High-Throughput Nucleotide Sequencing, Humans, Models, Genetic, Saccharomyces cerevisiae (genetics), Sequence Analysis, DNA, Software.
MESH :
- genetics : Burkholderia pseudomallei, Escherichia coli, Saccharomyces cerevisiae.
- methods : Contig Mapping.
- Algorithms, Computer Simulation, Genome, High-Throughput Nucleotide Sequencing, Humans, Models, Genetic, Sequence Analysis, DNA, Software.

Abstract

Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).

DOI: 10.1089/cmb.2011.0170
PubMed: 21929371

Affiliations:

Le document en format XML

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<author><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name>
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<term>Burkholderia pseudomallei (genetics)</term>
<term>Computer Simulation</term>
<term>Contig Mapping (methods)</term>
<term>Escherichia coli (genetics)</term>
<term>Genome</term>
<term>High-Throughput Nucleotide Sequencing</term>
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<front><div type="abstract" xml:lang="en">Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).</div>
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Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

Source :

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

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