EPGA2: memory-efficient de novo assembler.
Identifieur interne : 001487 ( PubMed/Corpus ); précédent : 001486; suivant : 001488EPGA2: memory-efficient de novo assembler.
Auteurs : Junwei Luo ; Jianxin Wang ; Weilong Li ; Zhen Zhang ; Fang-Xiang Wu ; Min Li ; Yi PanSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- methods : Genomics.
- Algorithms, Sequence Analysis, DNA, Software.
Abstract
In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.
DOI: 10.1093/bioinformatics/btv487
PubMed: 26315905
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">EPGA2: memory-efficient de novo assembler.</title><author><name sortKey="Luo, Junwei" sort="Luo, Junwei" uniqKey="Luo J" first="Junwei" last="Luo">Junwei Luo</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Jianxin" sort="Wang, Jianxin" uniqKey="Wang J" first="Jianxin" last="Wang">Jianxin Wang</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Weilong" sort="Li, Weilong" uniqKey="Li W" first="Weilong" last="Li">Weilong Li</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Zhen" sort="Zhang, Zhen" uniqKey="Zhang Z" first="Zhen" last="Zhang">Zhen Zhang</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Fang Xiang" sort="Wu, Fang Xiang" uniqKey="Wu F" first="Fang-Xiang" last="Wu">Fang-Xiang Wu</name><affiliation><nlm:affiliation>Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan, S7N 5A9, Canada and.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Min" sort="Li, Min" uniqKey="Li M" first="Min" last="Li">Min Li</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Yi" sort="Pan, Yi" uniqKey="Pan Y" first="Yi" last="Pan">Yi Pan</name><affiliation><nlm:affiliation>Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26315905</idno><idno type="pmid">26315905</idno><idno type="doi">10.1093/bioinformatics/btv487</idno><idno type="wicri:Area/PubMed/Corpus">001487</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001487</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">EPGA2: memory-efficient de novo assembler.</title><author><name sortKey="Luo, Junwei" sort="Luo, Junwei" uniqKey="Luo J" first="Junwei" last="Luo">Junwei Luo</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Jianxin" sort="Wang, Jianxin" uniqKey="Wang J" first="Jianxin" last="Wang">Jianxin Wang</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Weilong" sort="Li, Weilong" uniqKey="Li W" first="Weilong" last="Li">Weilong Li</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Zhen" sort="Zhang, Zhen" uniqKey="Zhang Z" first="Zhen" last="Zhang">Zhen Zhang</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wu, Fang Xiang" sort="Wu, Fang Xiang" uniqKey="Wu F" first="Fang-Xiang" last="Wu">Fang-Xiang Wu</name><affiliation><nlm:affiliation>Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan, S7N 5A9, Canada and.</nlm:affiliation></affiliation></author><author><name sortKey="Li, Min" sort="Li, Min" uniqKey="Li M" first="Min" last="Li">Min Li</name><affiliation><nlm:affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Yi" sort="Pan, Yi" uniqKey="Pan Y" first="Yi" last="Pan">Yi Pan</name><affiliation><nlm:affiliation>Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2015" type="published">2015</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</term><term>Software</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Sequence Analysis, DNA</term><term>Software</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">26315905</PMID><DateCompleted><Year>2016</Year><Month>08</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>31</Volume><Issue>24</Issue><PubDate><Year>2015</Year><Month>Dec</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>EPGA2: memory-efficient de novo assembler.</ArticleTitle><Pagination><MedlinePgn>3988-90</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btv487</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">In this article, we present an update algorithm called EPGA2, which applies some new modules and can bring about improved assembly results in small memory. For reducing peak memory in genome assembly, EPGA2 adopts memory-efficient DSK to count K-mers and revised BCALM to construct De Bruijn Graph. Moreover, EPGA2 parallels the step of Contigs Merging and adds Errors Correction in its pipeline. Our experiments demonstrate that all these changes in EPGA2 are more useful for genome assembly.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">EPGA2 is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA2.</AbstractText><CopyrightInformation>© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Junwei</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China, College of Computer Science and Technology, Henan Polytechnic University, JiaoZuo, 454000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jianxin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Weilong</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhen</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Fang-Xiang</ForeName><Initials>FX</Initials><AffiliationInfo><Affiliation>Division of Biomedical Engineering, University of Saskatchewan, Saskatchewan, S7N 5A9, Canada and.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Min</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>School of Information Science and Engineering, Central South University, ChangSha, 410083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA.</Affiliation></AffiliationInfo></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>2015</Year><Month>08</Month><Day>26</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></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>06</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>8</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>8</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26315905</ArticleId><ArticleId IdType="pii">btv487</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btv487</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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