Reptile: representative tiling for short read error correction.
Identifieur interne : 000773 ( Ncbi/Merge ); précédent : 000772; suivant : 000774Reptile: representative tiling for short read error correction.
Auteurs : Xiao Yang [États-Unis] ; Karin S. Dorman ; Srinivas AluruSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Genomics, Sequence Analysis, DNA.
- Algorithms, Software.
Abstract
Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error correction methods is both compute and memory intensive, yet the results are far from satisfactory when applied to real datasets.
DOI: 10.1093/bioinformatics/btq468
PubMed: 20834037
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pubmed:20834037Le document en format XML
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Dorman</name></author><author><name sortKey="Aluru, Srinivas" sort="Aluru, Srinivas" uniqKey="Aluru S" first="Srinivas" last="Aluru">Srinivas Aluru</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20834037</idno><idno type="pmid">20834037</idno><idno type="doi">10.1093/bioinformatics/btq468</idno><idno type="wicri:Area/PubMed/Corpus">001F38</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F38</idno><idno type="wicri:Area/PubMed/Curation">001F38</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F38</idno><idno type="wicri:Area/PubMed/Checkpoint">001E23</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E23</idno><idno type="wicri:Area/Ncbi/Merge">000773</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Reptile: representative tiling for short read error correction.</title><author><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name><affiliation wicri:level="4"><nlm:affiliation>Department of Electrical and Computer Engineering, Iowa State University, Ames IA 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Electrical and Computer Engineering, Iowa State University, Ames IA 50011</wicri:regionArea><orgName type="university">Université d'État de l'Iowa</orgName><placeName><settlement type="city">Ames (Iowa)</settlement><region type="state">Iowa</region></placeName></affiliation></author><author><name sortKey="Dorman, Karin S" sort="Dorman, Karin S" uniqKey="Dorman K" first="Karin S" last="Dorman">Karin S. Dorman</name></author><author><name sortKey="Aluru, Srinivas" sort="Aluru, Srinivas" uniqKey="Aluru S" first="Srinivas" last="Aluru">Srinivas Aluru</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Genomics (methods)</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>Génomique ()</term><term>Logiciel</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Génomique</term><term>Logiciel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error correction methods is both compute and memory intensive, yet the results are far from satisfactory when applied to real datasets.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20834037</PMID><DateCompleted><Year>2011</Year><Month>02</Month><Day>16</Day></DateCompleted><DateRevised><Year>2010</Year><Month>10</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><Issue>20</Issue><PubDate><Year>2010</Year><Month>Oct</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Reptile: representative tiling for short read error correction.</ArticleTitle><Pagination><MedlinePgn>2526-33</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btq468</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error correction methods is both compute and memory intensive, yet the results are far from satisfactory when applied to real datasets.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We present a novel approach, termed Reptile, for error correction in short-read data from next-generation sequencing. Reptile works with the spectrum of k-mers from the input reads, and corrects errors by simultaneously examining: (i) Hamming distance-based correction possibilities for potentially erroneous k-mers; and (ii) neighboring k-mers from the same read for correct contextual information. By not needing to store input data, Reptile has the favorable property that it can handle data that does not fit in main memory. In addition to sequence data, Reptile can make use of available quality score information. Our experiments show that Reptile outperforms previous methods in the percentage of errors removed from the data and the accuracy in true base assignment. In addition, a significant reduction in run time and memory usage have been achieved compared with previous methods, making it more practical for short-read error correction when sampling larger genomes.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">Reptile is implemented in C++ and is available through the link: http://aluru-sun.ece.iastate.edu/doku.php?id=software</AbstractText><AbstractText Label="CONTACT" NlmCategory="BACKGROUND">aluru@iastate.edu.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Electrical and Computer Engineering, Iowa State University, Ames IA 50011, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dorman</LastName><ForeName>Karin S</ForeName><Initials>KS</Initials></Author><Author ValidYN="Y"><LastName>Aluru</LastName><ForeName>Srinivas</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>08</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>9</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>9</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>2</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20834037</ArticleId><ArticleId IdType="pii">btq468</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btq468</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Iowa</li></region><settlement><li>Ames (Iowa)</li></settlement><orgName><li>Université d'État de l'Iowa</li></orgName></list><tree><noCountry><name sortKey="Aluru, Srinivas" sort="Aluru, Srinivas" uniqKey="Aluru S" first="Srinivas" last="Aluru">Srinivas Aluru</name><name sortKey="Dorman, Karin S" sort="Dorman, Karin S" uniqKey="Dorman K" first="Karin S" last="Dorman">Karin S. Dorman</name></noCountry><country name="États-Unis"><region name="Iowa"><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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