Readjoiner: a fast and memory efficient string graph-based sequence assembler
Identifieur interne : 000956 ( Ncbi/Checkpoint ); précédent : 000955; suivant : 000957Readjoiner: 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
Affiliations:
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PMC:3507659Le document en format XML
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first="Giorgio" last="Gonnella">Giorgio Gonnella</name><affiliation wicri:level="3"><nlm:aff id="I1">Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg</wicri:regionArea><placeName><settlement type="city">Hambourg</settlement><region type="land" nuts="2">Hambourg</region></placeName></affiliation></author><author><name sortKey="Kurtz, Stefan" sort="Kurtz, Stefan" uniqKey="Kurtz S" first="Stefan" last="Kurtz">Stefan Kurtz</name><affiliation wicri:level="3"><nlm:aff id="I1">Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Center for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146, Hamburg</wicri:regionArea><placeName><settlement type="city">Hambourg</settlement><region type="land" nuts="2">Hambourg</region></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Genome, Human (genetics)</term><term>Humans</term><term>Models, Genetic</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Génome humain (génétique)</term><term>Humains</term><term>Logiciel</term><term>Modèles génétiques</term><term>Simulation numérique</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Human</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Génome humain</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Computer Simulation</term><term>Humans</term><term>Models, Genetic</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Logiciel</term><term>Modèles génétiques</term><term>Simulation numérique</term></keywords></textClass></profileDesc></teiHeader><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></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Myers, Ew" uniqKey="Myers E">EW Myers</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Mcpherson, Jd" uniqKey="Mcpherson J">JD McPherson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name></author><author><name sortKey="Tang, H" uniqKey="Tang H">H Tang</name></author><author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zerbino, Dr" uniqKey="Zerbino D">DR Zerbino</name></author><author><name sortKey="Birney, E" uniqKey="Birney E">E 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Lavenier</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Hambourg</li></region><settlement><li>Hambourg</li></settlement></list><tree><country name="Allemagne"><region name="Hambourg"><name sortKey="Gonnella, Giorgio" sort="Gonnella, Giorgio" uniqKey="Gonnella G" first="Giorgio" last="Gonnella">Giorgio Gonnella</name></region><name sortKey="Kurtz, Stefan" sort="Kurtz, Stefan" uniqKey="Kurtz S" first="Stefan" last="Kurtz">Stefan Kurtz</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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