Readjoiner: a fast and memory efficient string graph-based sequence assembler
Identifieur interne : 002216 ( Main/Curation ); précédent : 002215; suivant : 002217Readjoiner: a fast and memory efficient string graph-based sequence assembler
Auteurs : Giorgio Gonnella [Allemagne] ; Stefan Kurtz [Allemagne]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
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.
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
Url:
DOI: 10.1186/1471-2105-13-82
PubMed: 22559072
PubMed Central: 3507659
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PMC:3507659Le document en format XML
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<term>Sequence Analysis, DNA (methods)</term>
<term>Software</term>
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<term>Humains</term>
<term>Logiciel</term>
<term>Modèles génétiques</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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 <italic>k</italic>
-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads.</p>
</sec>
<sec><title>Results</title>
<p>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.</p>
</sec>
<sec><title>Conclusions</title>
<p>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 <ext-link ext-link-type="uri" xlink:href="http://www.zbh.uni-hamburg.de/readjoiner">http://www.zbh.uni-hamburg.de/readjoiner</ext-link>
.</p>
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<author><name sortKey="Green, R" uniqKey="Green R">R Green</name>
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<author><name sortKey="Haussler, D" uniqKey="Haussler D">D Haussler</name>
</author>
<author><name sortKey="Korf, I" uniqKey="Korf I">I Korf</name>
</author>
<author><name sortKey="Paten, B" uniqKey="Paten B">B Paten</name>
</author>
</analytic>
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</author>
<author><name sortKey="Landau, Gm" uniqKey="Landau G">GM Landau</name>
</author>
<author><name sortKey="Schieber, B" uniqKey="Schieber B">B Schieber</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ohlebusch, E" uniqKey="Ohlebusch E">E Ohlebusch</name>
</author>
<author><name sortKey="Gog, S" uniqKey="Gog S">S Gog</name>
</author>
</analytic>
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<biblStruct><analytic><author><name sortKey="Kelley, D" uniqKey="Kelley D">D Kelley</name>
</author>
<author><name sortKey="Schatz, M" uniqKey="Schatz M">M Schatz</name>
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<author><name sortKey="Salzberg, S" uniqKey="Salzberg S">S Salzberg</name>
</author>
</analytic>
</biblStruct>
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<author><name sortKey="Kosack, Ds" uniqKey="Kosack D">DS Kosack</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
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</author>
<author><name sortKey="Henkel, Cv" uniqKey="Henkel C">CV Henkel</name>
</author>
<author><name sortKey="Jansen, Hj" uniqKey="Jansen H">HJ Jansen</name>
</author>
<author><name sortKey="Butler, D" uniqKey="Butler D">D Butler</name>
</author>
<author><name sortKey="Pirovano, W" uniqKey="Pirovano W">W Pirovano</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Donmez, N" uniqKey="Donmez N">N Donmez</name>
</author>
<author><name sortKey="Brudno, M" uniqKey="Brudno M">M Brudno</name>
</author>
</analytic>
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</author>
<author><name sortKey="Lavenier, D" uniqKey="Lavenier D">D Lavenier</name>
</author>
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</back>
</TEI>
</record>
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