Accelerating metagenomic read classification on CUDA-enabled GPUs
Identifieur interne : 000F02 ( Main/Exploration ); précédent : 000F01; suivant : 000F03Accelerating 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
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.
We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced
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
Url:
DOI: 10.1186/s12859-016-1434-6
PubMed: 28049411
PubMed Central: 5209836
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000262
- to stream Pmc, to step Curation: 000262
- to stream Pmc, to step Checkpoint: 000935
- to stream PubMed, to step Corpus: 000E27
- to stream PubMed, to step Curation: 000E27
- to stream PubMed, to step Checkpoint: 000E02
- to stream Ncbi, to step Merge: 001903
- to stream Ncbi, to step Curation: 001903
- to stream Ncbi, to step Checkpoint: 001903
- to stream Main, to step Merge: 000F05
- to stream Main, to step Curation: 000F02
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Accelerating metagenomic read classification on CUDA-enabled GPUs</title><author><name sortKey="Kobus, Robin" sort="Kobus, Robin" uniqKey="Kobus R" first="Robin" last="Kobus">Robin Kobus</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Hundt, Christian" sort="Hundt, Christian" uniqKey="Hundt C" first="Christian" last="Hundt">Christian Hundt</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Muller, Andre" sort="Muller, Andre" uniqKey="Muller A" first="André" last="Müller">André Müller</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28049411</idno><idno type="pmc">5209836</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209836</idno><idno type="RBID">PMC:5209836</idno><idno type="doi">10.1186/s12859-016-1434-6</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">000262</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000262</idno><idno type="wicri:Area/Pmc/Curation">000262</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000262</idno><idno type="wicri:Area/Pmc/Checkpoint">000935</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000935</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:28049411</idno><idno type="wicri:Area/PubMed/Corpus">000E27</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E27</idno><idno type="wicri:Area/PubMed/Curation">000E27</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E27</idno><idno type="wicri:Area/PubMed/Checkpoint">000E02</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000E02</idno><idno type="wicri:Area/Ncbi/Merge">001903</idno><idno type="wicri:Area/Ncbi/Curation">001903</idno><idno type="wicri:Area/Ncbi/Checkpoint">001903</idno><idno type="wicri:Area/Main/Merge">000F05</idno><idno type="wicri:Area/Main/Curation">000F02</idno><idno type="wicri:Area/Main/Exploration">000F02</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Accelerating metagenomic read classification on CUDA-enabled GPUs</title><author><name sortKey="Kobus, Robin" sort="Kobus, Robin" uniqKey="Kobus R" first="Robin" last="Kobus">Robin Kobus</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Hundt, Christian" sort="Hundt, Christian" uniqKey="Hundt C" first="Christian" last="Hundt">Christian Hundt</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Muller, Andre" sort="Muller, Andre" uniqKey="Muller A" first="André" last="Müller">André Müller</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author><author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz, 55435 Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Computer Science, Johannes Gutenberg University Mainz, Staudingerweg 9, Mainz</wicri:regionArea><placeName><region type="land" nuts="2">Rhénanie-Palatinat</region><settlement type="city">Mayence</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2017">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"><sec><title>Background</title><p>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.</p></sec><sec><title>Results</title><p>We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced <italic>k</italic>-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.</p></sec><sec><title>Conclusion</title><p>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 <ext-link ext-link-type="uri" xlink:href="https://github.com/funatiq/cuclark">https://github.com/funatiq/cuclark</ext-link> free of charge.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ounit, R" uniqKey="Ounit R">R Ounit</name></author><author><name sortKey="Wanamaker, S" uniqKey="Wanamaker S">S Wanamaker</name></author><author><name sortKey="Close, Tj" uniqKey="Close T">TJ Close</name></author><author><name sortKey="Lonardi, S" uniqKey="Lonardi S">S Lonardi</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Wilton, R" uniqKey="Wilton R">R Wilton</name></author><author><name sortKey="Budavari, T" uniqKey="Budavari T">T Budavari</name></author><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name></author><author><name sortKey="Wheelan, Sj" uniqKey="Wheelan S">SJ Wheelan</name></author><author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name></author><author><name sortKey="Szalay, As" uniqKey="Szalay A">AS Szalay</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Liu, Y" uniqKey="Liu Y">Y Liu</name></author><author><name sortKey="Schmidt, B" uniqKey="Schmidt B">B Schmidt</name></author><author><name sortKey="Maskell, Dl" uniqKey="Maskell D">DL Maskell</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Li, D" uniqKey="Li D">D Li</name></author><author><name sortKey="Liu, Cm" uniqKey="Liu C">CM Liu</name></author><author><name sortKey="Luo, R" uniqKey="Luo R">R Luo</name></author><author><name sortKey="Sadakane, K" uniqKey="Sadakane K">K Sadakane</name></author><author><name sortKey="Lam, Tw" uniqKey="Lam T">TW Lam</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Huang, W" uniqKey="Huang W">W Huang</name></author><author><name sortKey="Li, L" uniqKey="Li L">L Li</name></author><author><name sortKey="Myers, Jr" uniqKey="Myers J">JR Myers</name></author><author><name sortKey="Marth, Gt" uniqKey="Marth G">GT Marth</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Shcherbina, A" uniqKey="Shcherbina A">A Shcherbina</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Rhénanie-Palatinat</li></region><settlement><li>Mayence</li></settlement></list><tree><country name="Allemagne"><region name="Rhénanie-Palatinat"><name sortKey="Kobus, Robin" sort="Kobus, Robin" uniqKey="Kobus R" first="Robin" last="Kobus">Robin Kobus</name></region><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)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000F02 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000F02 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:5209836
|texte= Accelerating metagenomic read classification on CUDA-enabled GPUs
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:28049411" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |