Accelerating metagenomic read classification on CUDA-enabled GPUs
Identifieur interne : 000F02 ( Main/Curation ); 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.
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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.
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
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PMC:5209836Le document en format XML
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<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>
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<author><name sortKey="Hundt, Christian" sort="Hundt, Christian" uniqKey="Hundt C" first="Christian" last="Hundt">Christian Hundt</name>
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<author><name sortKey="Schmidt, Bertil" sort="Schmidt, Bertil" uniqKey="Schmidt B" first="Bertil" last="Schmidt">Bertil Schmidt</name>
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<series><title level="j">BMC Bioinformatics</title>
<idno type="eISSN">1471-2105</idno>
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<term>Humans</term>
<term>Internet</term>
<term>Metagenomics</term>
<term>Sequence Analysis, DNA</term>
<term>User-Computer Interface</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Humains</term>
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<term>Internet</term>
<term>Métagénomique</term>
<term>Séquençage nucléotidique à haut débit</term>
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<keywords scheme="MESH" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term>
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<term>Internet</term>
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<term>User-Computer Interface</term>
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<term>Humains</term>
<term>Interface utilisateur</term>
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<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>
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</author>
<author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name>
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<author><name sortKey="Wheelan, Sj" uniqKey="Wheelan S">SJ Wheelan</name>
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<author><name sortKey="Maskell, Dl" uniqKey="Maskell D">DL Maskell</name>
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<author><name sortKey="Luo, R" uniqKey="Luo R">R Luo</name>
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<author><name sortKey="Sadakane, K" uniqKey="Sadakane K">K Sadakane</name>
</author>
<author><name sortKey="Lam, Tw" uniqKey="Lam T">TW Lam</name>
</author>
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</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>
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</biblStruct>
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