Accelerating metagenomic read classification on CUDA-enabled GPUs.
Identifieur interne : 000E02 ( PubMed/Checkpoint ); précédent : 000E01; suivant : 000E03Accelerating metagenomic read classification on CUDA-enabled GPUs.
Auteurs : Robin Kobus [Allemagne] ; Christian Hundt [Allemagne] ; André Müller [Allemagne] ; Bertil Schmidt [Allemagne]Source :
- BMC bioinformatics [ 1471-2105 ] ; 2017.
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Abstract
Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed.
DOI: 10.1186/s12859-016-1434-6
PubMed: 28049411
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xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435</wicri:regionArea><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion></affiliation></author><author><name sortKey="Hundt, Christian" sort="Hundt, Christian" uniqKey="Hundt C" first="Christian" last="Hundt">Christian Hundt</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435</wicri:regionArea><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion></affiliation></author><author><name sortKey="Muller, Andre" sort="Muller, Andre" uniqKey="Muller A" first="André" last="Müller">André Müller</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435</wicri:regionArea><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435</wicri:regionArea><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion><wicri:noRegion>55435</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Internet</term><term>Metagenomics</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique</term><term>Séquençage nucléotidique à haut débit</term></keywords><keywords scheme="MESH" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term><term>Humans</term><term>Internet</term><term>Metagenomics</term><term>Sequence Analysis, DNA</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Humains</term><term>Interface utilisateur</term><term>Internet</term><term>Métagénomique</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">28049411</PMID><DateCompleted><Year>2017</Year><Month>08</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>18</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Jan</Month><Day>03</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Accelerating metagenomic read classification on CUDA-enabled GPUs.</ArticleTitle><Pagination><MedlinePgn>11</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12859-016-1434-6</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (CLARK) method. Using the processing power of a single Titan X GPU, cuCLARK can reach classification speeds of up to 50 million reads per minute. Corresponding speedups for species- (genus-)level classification range between 3.2 and 6.6 (3.7 and 6.4) compared to multi-threaded CLARK executed on a 16-core Xeon CPU workstation.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">cuCLARK can perform metagenomic read classification at superior speeds on CUDA-enabled GPUs. It is free software licensed under GPL and can be downloaded at https://github.com/funatiq/cuclark free of charge.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kobus</LastName><ForeName>Robin</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany. rkobus@students.uni-mainz.de.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hundt</LastName><ForeName>Christian</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Müller</LastName><ForeName>André</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435, Germany.</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, Staudingerweg 9, Mainz, 55435, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>01</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="Y">Metagenomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014584" MajorTopicYN="Y">User-Computer Interface</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">CUDA</Keyword><Keyword MajorTopicYN="N">Exact k-mer matching</Keyword><Keyword MajorTopicYN="N">GPUs</Keyword><Keyword MajorTopicYN="N">Metagenomics</Keyword><Keyword MajorTopicYN="N">Taxonomic assignment</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>09</Month><Day>09</Day></PubMedPubDate><PubMedPubDate 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IdType="pubmed">22199392</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Kobus, Robin" sort="Kobus, Robin" uniqKey="Kobus R" first="Robin" last="Kobus">Robin Kobus</name></noRegion><name sortKey="Hundt, Christian" sort="Hundt, Christian" uniqKey="Hundt C" first="Christian" last="Hundt">Christian Hundt</name><name sortKey="Muller, Andre" sort="Muller, Andre" uniqKey="Muller A" first="André" last="Müller">André Müller</name><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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