IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Identifieur interne : 001C76 ( PubMed/Checkpoint ); précédent : 001C75; suivant : 001C77IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Auteurs : Yu Peng [Hong Kong] ; Henry C M. Leung ; S M Yiu ; Francis Y L. ChinSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Bacteria.
- methods : Metagenomics, Sequence Analysis, DNA, Single-Cell Analysis.
- Algorithms, Genome, High-Throughput Nucleotide Sequencing.
Abstract
Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.
DOI: 10.1093/bioinformatics/bts174
PubMed: 22495754
Affiliations:
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Leung</name></author><author><name sortKey="Yiu, S M" sort="Yiu, S M" uniqKey="Yiu S" first="S M" last="Yiu">S M Yiu</name></author><author><name sortKey="Chin, Francis Y L" sort="Chin, Francis Y L" uniqKey="Chin F" first="Francis Y L" last="Chin">Francis Y L. Chin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22495754</idno><idno type="pmid">22495754</idno><idno type="doi">10.1093/bioinformatics/bts174</idno><idno type="wicri:Area/PubMed/Corpus">001D89</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D89</idno><idno type="wicri:Area/PubMed/Curation">001D89</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001D89</idno><idno type="wicri:Area/PubMed/Checkpoint">001C76</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001C76</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.</title><author><name sortKey="Peng, Yu" sort="Peng, Yu" uniqKey="Peng Y" first="Yu" last="Peng">Yu Peng</name><affiliation wicri:level="1"><nlm:affiliation>Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong.</nlm:affiliation><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Computer Science, The University of Hong Kong, Pokfulam Road</wicri:regionArea><wicri:noRegion>Pokfulam Road</wicri:noRegion></affiliation></author><author><name sortKey="Leung, Henry C M" sort="Leung, Henry C M" uniqKey="Leung H" first="Henry C M" last="Leung">Henry C M. Leung</name></author><author><name sortKey="Yiu, S M" sort="Yiu, S M" uniqKey="Yiu S" first="S M" last="Yiu">S M Yiu</name></author><author><name sortKey="Chin, Francis Y L" sort="Chin, Francis Y L" uniqKey="Chin F" first="Francis Y L" last="Chin">Francis Y L. Chin</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Bacteria (genetics)</term><term>Genome</term><term>High-Throughput Nucleotide Sequencing</term><term>Metagenomics (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Single-Cell Analysis (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Analyse sur cellule unique ()</term><term>Bactéries (génétique)</term><term>Génome</term><term>Métagénomique ()</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term><term>Sequence Analysis, DNA</term><term>Single-Cell Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Genome</term><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Analyse sur cellule unique</term><term>Génome</term><term>Métagénomique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">22495754</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>28</Volume><Issue>11</Issue><PubDate><Year>2012</Year><Month>Jun</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.</ArticleTitle><Pagination><MedlinePgn>1420-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bts174</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Peng</LastName><ForeName>Yu</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Leung</LastName><ForeName>Henry C M</ForeName><Initials>HC</Initials></Author><Author ValidYN="Y"><LastName>Yiu</LastName><ForeName>S M</ForeName><Initials>SM</Initials></Author><Author ValidYN="Y"><LastName>Chin</LastName><ForeName>Francis Y L</ForeName><Initials>FY</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>2012</Year><Month>04</Month><Day>11</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="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001419" MajorTopicYN="N">Bacteria</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="N">Metagenomics</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="D059010" MajorTopicYN="N">Single-Cell Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>4</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>4</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>2</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22495754</ArticleId><ArticleId IdType="pii">bts174</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/bts174</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Hong Kong</li></country></list><tree><noCountry><name sortKey="Chin, Francis Y L" sort="Chin, Francis Y L" uniqKey="Chin F" first="Francis Y L" last="Chin">Francis Y L. Chin</name><name sortKey="Leung, Henry C M" sort="Leung, Henry C M" uniqKey="Leung H" first="Henry C M" last="Leung">Henry C M. Leung</name><name sortKey="Yiu, S M" sort="Yiu, S M" uniqKey="Yiu S" first="S M" last="Yiu">S M Yiu</name></noCountry><country name="Hong Kong"><noRegion><name sortKey="Peng, Yu" sort="Peng, Yu" uniqKey="Peng Y" first="Yu" last="Peng">Yu Peng</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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