kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
Identifieur interne : 000550 ( PubMed/Curation ); précédent : 000549; suivant : 000551kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.
Auteurs : Peng Jiang [République populaire de Chine] ; Jie Luo [République populaire de Chine] ; Yiqi Wang [République populaire de Chine] ; Pingji Deng [République populaire de Chine] ; Bertil Schmidt ; Xiangjun Tang [République populaire de Chine] ; Ningjiang Chen [République populaire de Chine] ; Limsoon Wong [Singapour] ; Liang Zhao [République populaire de Chine]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2019.
Abstract
K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability.
DOI: 10.1093/bioinformatics/btz299
PubMed: 31038666
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Bertil Schmidt<affiliation><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz Germany.</nlm:affiliation><wicri:noCountry code="subField">Mainz Germany</wicri:noCountry></affiliation>Le document en format XML
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Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz Germany.</nlm:affiliation><wicri:noCountry code="subField">Mainz Germany</wicri:noCountry></affiliation></author><author><name sortKey="Tang, Xiangjun" sort="Tang, Xiangjun" uniqKey="Tang X" first="Xiangjun" last="Tang">Xiangjun Tang</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ningjiang" sort="Chen, Ningjiang" uniqKey="Chen N" first="Ningjiang" last="Chen">Ningjiang Chen</name><affiliation wicri:level="1"><nlm:affiliation>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Limsoon" sort="Wong, Limsoon" uniqKey="Wong L" first="Limsoon" last="Wong">Limsoon Wong</name><affiliation wicri:level="1"><nlm:affiliation>School of Computing, National University of Singapore, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Liang" sort="Zhao, Liang" uniqKey="Zhao L" first="Liang" last="Zhao">Liang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31038666</idno><idno type="pmid">31038666</idno><idno type="doi">10.1093/bioinformatics/btz299</idno><idno type="wicri:Area/PubMed/Corpus">000550</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000550</idno><idno type="wicri:Area/PubMed/Curation">000550</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000550</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.</title><author><name sortKey="Jiang, Peng" sort="Jiang, Peng" uniqKey="Jiang P" first="Peng" last="Jiang">Peng Jiang</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Luo, Jie" sort="Luo, Jie" uniqKey="Luo J" first="Jie" last="Luo">Jie Luo</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Wang, Yiqi" sort="Wang, Yiqi" uniqKey="Wang Y" first="Yiqi" last="Wang">Yiqi Wang</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Deng, Pingji" sort="Deng, Pingji" uniqKey="Deng P" first="Pingji" last="Deng">Pingji Deng</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz Germany.</nlm:affiliation><wicri:noCountry code="subField">Mainz Germany</wicri:noCountry></affiliation></author><author><name sortKey="Tang, Xiangjun" sort="Tang, Xiangjun" uniqKey="Tang X" first="Xiangjun" last="Tang">Xiangjun Tang</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author><author><name sortKey="Chen, Ningjiang" sort="Chen, Ningjiang" uniqKey="Chen N" first="Ningjiang" last="Chen">Ningjiang Chen</name><affiliation wicri:level="1"><nlm:affiliation>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi</wicri:regionArea></affiliation></author><author><name sortKey="Wong, Limsoon" sort="Wong, Limsoon" uniqKey="Wong L" first="Limsoon" last="Wong">Limsoon Wong</name><affiliation wicri:level="1"><nlm:affiliation>School of Computing, National University of Singapore, Singapore, Singapore.</nlm:affiliation><country xml:lang="fr">Singapour</country><wicri:regionArea>School of Computing, National University of Singapore, Singapore</wicri:regionArea></affiliation></author><author><name sortKey="Zhao, Liang" sort="Zhao, Liang" uniqKey="Zhao L" first="Liang" last="Zhao">Liang Zhao</name><affiliation wicri:level="1"><nlm:affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei</wicri:regionArea></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">31038666</PMID><DateRevised><Year>2020</Year><Month>01</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>35</Volume><Issue>23</Issue><PubDate><Year>2019</Year><Month>Dec</Month><Day>01</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers.</ArticleTitle><Pagination><MedlinePgn>4871-4878</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz299</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">K-mers along with their frequency have served as an elementary building block for error correction, repeat detection, multiple sequence alignment, genome assembly, etc., attracting intensive studies in k-mer counting. However, the output of k-mer counters itself is large; very often, it is too large to fit into main memory, leading to highly narrowed usability.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce a novel idea of encoding k-mers as well as their frequency, achieving good memory saving and retrieval efficiency. Specifically, we propose a Bloom filter-like data structure to encode counted k-mers by coupled-bit arrays-one for k-mer representation and the other for frequency encoding. Experiments on five real datasets show that the average memory-saving ratio on all 31-mers is as high as 13.81 as compared with raw input, with 7 hash functions. At the same time, the retrieval time complexity is well controlled (effectively constant), and the false-positive rate is decreased by two orders of magnitude.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">The source codes of our algorithm are available at github.com/lzhLab/kmcEx.</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author(s) 2019. 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>Jiang</LastName><ForeName>Peng</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Jie</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yiqi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deng</LastName><ForeName>Pingji</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schmidt</LastName><ForeName>Bertil</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Mainz Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Xiangjun</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Ningjiang</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Limsoon</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>School of Computing, National University of Singapore, Singapore, Singapore.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Liang</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Computing and Electronic Information, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>06</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>04</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>04</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31038666</ArticleId><ArticleId IdType="pii">5481953</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btz299</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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