MersV1, PubMed, Checkpoint, bibRecord, 001C42

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Identifieur interne : 001C42 ( PubMed/Checkpoint ); précédent : 001C41; suivant : 001C43

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Auteurs : Giorgio Gonnella [Allemagne] ; Stefan Kurtz

Source :

BMC bioinformatics [ 1471-2105 ] ; 2012.

RBID : pubmed:22559072

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN (), Génome humain (génétique), Humains, Logiciel, Modèles génétiques, Simulation numérique.
MESH :
- génétique : Génome humain.
- Algorithmes, Analyse de séquence d'ADN, Humains, Logiciel, Modèles génétiques, Simulation numérique.

English descriptors

KwdEn :
- Algorithms, Computer Simulation, Genome, Human (genetics), Humans, Models, Genetic, Sequence Analysis, DNA (methods), Software.
MESH :
- genetics : Genome, Human.
- methods : Sequence Analysis, DNA.
- Algorithms, Computer Simulation, Humans, Models, Genetic, Software.

Abstract

Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads.

DOI: 10.1186/1471-2105-13-82
PubMed: 22559072

Affiliations:

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Le document en format XML

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<term>Analyse de séquence d'ADN</term>
<term>Humains</term>
<term>Logiciel</term>
<term>Modèles génétiques</term>
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<front><div type="abstract" xml:lang="en">Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads.</div>
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<Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">Here we present efficient methods for the construction of a string graph from a set of sequencing reads. Our approach employs suffix sorting and scanning methods to compute suffix-prefix matches. Transitive edges are recognized and eliminated early in the process and the graph is efficiently constructed including irreducible edges only.</AbstractText>
<AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our suffix-prefix match determination and string graph construction algorithms have been implemented in the software package Readjoiner. Comparison with existing string graph-based assemblers shows that Readjoiner is faster and more space efficient. Readjoiner is available at http://www.zbh.uni-hamburg.de/readjoiner.</AbstractText>
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Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Source :

Descripteurs français

English descriptors

Abstract

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

Links to Exploration step

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