RepARK—de novo creation of repeat libraries from whole-genome NGS reads
Identifieur interne : 001B03 ( Main/Exploration ); précédent : 001B02; suivant : 001B04RepARK—de novo creation of repeat libraries from whole-genome NGS reads
Auteurs : Philipp Koch ; Matthias Platzer ; Bryan R. DownieSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2014.
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Abstract
Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a
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DOI: 10.1093/nar/gku210
PubMed: 24634442
PubMed Central: 4027187
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RepARK—<italic>de novo</italic> creation of repeat libraries from whole-genome NGS reads</title><author><name sortKey="Koch, Philipp" sort="Koch, Philipp" uniqKey="Koch P" first="Philipp" last="Koch">Philipp Koch</name></author><author><name sortKey="Platzer, Matthias" sort="Platzer, Matthias" uniqKey="Platzer M" first="Matthias" last="Platzer">Matthias Platzer</name></author><author><name sortKey="Downie, Bryan R" sort="Downie, Bryan R" uniqKey="Downie B" first="Bryan R." last="Downie">Bryan R. 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Downie</name></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chromosome Mapping</term><term>Computer Simulation</term><term>Consensus Sequence</term><term>Genomic Library</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Models, Genetic</term><term>Molecular Sequence Annotation</term><term>Repetitive Sequences, Nucleic Acid</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Banque génomique</term><term>Cartographie chromosomique</term><term>Humains</term><term>Logiciel</term><term>Modèles génétiques</term><term>Simulation numérique</term><term>Séquence consensus</term><term>Séquences répétées d'acides nucléiques</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Chromosome Mapping</term><term>Computer Simulation</term><term>Consensus Sequence</term><term>Genomic Library</term><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Models, Genetic</term><term>Molecular Sequence Annotation</term><term>Repetitive Sequences, Nucleic Acid</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Banque génomique</term><term>Cartographie chromosomique</term><term>Humains</term><term>Logiciel</term><term>Modèles génétiques</term><term>Simulation numérique</term><term>Séquence consensus</term><term>Séquences répétées d'acides nucléiques</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a <italic>de novo</italic> repeat assembly method—RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)—which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real <italic>Drosophila melanogaster</italic> NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lander, E S" uniqKey="Lander E">E.S. Lander</name></author><author><name sortKey="Linton, L M" uniqKey="Linton L">L.M. Linton</name></author><author><name sortKey="Birren, B" uniqKey="Birren B">B. Birren</name></author><author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C. Nusbaum</name></author><author><name sortKey="Zody, M C" uniqKey="Zody M">M.C. Zody</name></author><author><name sortKey="Baldwin, J" uniqKey="Baldwin J">J. Baldwin</name></author><author><name sortKey="Devon, K" uniqKey="Devon K">K. Devon</name></author><author><name sortKey="Dewar, K" uniqKey="Dewar K">K. Dewar</name></author><author><name sortKey="Doyle, M" uniqKey="Doyle M">M. 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Quesneville</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, C D" uniqKey="Smith C">C.D. Smith</name></author><author><name sortKey="Shu, S" uniqKey="Shu S">S. Shu</name></author><author><name sortKey="Mungall, C J" uniqKey="Mungall C">C.J. Mungall</name></author><author><name sortKey="Karpen, G H" uniqKey="Karpen G">G.H. Karpen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bennett, E A" uniqKey="Bennett E">E.A. Bennett</name></author><author><name sortKey="Keller, H" uniqKey="Keller H">H. Keller</name></author><author><name sortKey="Mills, R E" uniqKey="Mills R">R.E. Mills</name></author><author><name sortKey="Schmidt, S" uniqKey="Schmidt S">S. Schmidt</name></author><author><name sortKey="Moran, J V" uniqKey="Moran J">J.V. Moran</name></author><author><name sortKey="Weichenrieder, O" uniqKey="Weichenrieder O">O. Weichenrieder</name></author><author><name sortKey="Devine, S E" uniqKey="Devine S">S.E. Devine</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Morissette, G" uniqKey="Morissette G">G. Morissette</name></author><author><name sortKey="Flamand, L" uniqKey="Flamand L">L. Flamand</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Downie, Bryan R" sort="Downie, Bryan R" uniqKey="Downie B" first="Bryan R." last="Downie">Bryan R. Downie</name><name sortKey="Koch, Philipp" sort="Koch, Philipp" uniqKey="Koch P" first="Philipp" last="Koch">Philipp Koch</name><name sortKey="Platzer, Matthias" sort="Platzer, Matthias" uniqKey="Platzer M" first="Matthias" last="Platzer">Matthias Platzer</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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