Ray Meta: scalable de novo metagenome assembly and profiling
Identifieur interne : 001286 ( Pmc/Checkpoint ); précédent : 001285; suivant : 001287Ray Meta: scalable de novo metagenome assembly and profiling
Auteurs : Sébastien Boisvert [Canada] ; Frédéric Raymond [Canada] ; Élénie Godzaridis [Canada] ; François Laviolette [Canada] ; Jacques Corbeil [Canada]Source :
- Genome Biology [ 1465-6906 ] ; 2012.
Abstract
Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for
Url:
DOI: 10.1186/gb-2012-13-12-r122
PubMed: 23259615
PubMed Central: 4056372
Affiliations:
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PMC:4056372Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for <italic>de novo </italic>
assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at <ext-link ext-link-type="uri" xlink:href="http://denovoassembler.sf.net">http://denovoassembler.sf.net</ext-link>
.</p>
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</TEI>
<pmc article-type="research-article" xml:lang="en"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id>
<journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id>
<journal-title-group><journal-title>Genome Biology</journal-title>
</journal-title-group>
<issn pub-type="ppub">1465-6906</issn>
<issn pub-type="epub">1465-6914</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">23259615</article-id>
<article-id pub-id-type="pmc">4056372</article-id>
<article-id pub-id-type="publisher-id">gb-2012-13-12-r122</article-id>
<article-id pub-id-type="doi">10.1186/gb-2012-13-12-r122</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Method</subject>
</subj-group>
</article-categories>
<title-group><article-title>Ray Meta: scalable <italic>de novo </italic>
metagenome assembly and profiling</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Boisvert</surname>
<given-names>Sébastien</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>sebastien.boisvert.3@ulaval.ca</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Raymond</surname>
<given-names>Frédéric</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>frederic.raymond@crchul.ulaval.ca</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>Godzaridis</surname>
<given-names>Élénie</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>elenie.godzaridis.1@ulaval.ca</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Laviolette</surname>
<given-names>François</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>francois.laviolette@ift.ulaval.ca</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>Corbeil</surname>
<given-names>Jacques</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I4">4</xref>
<email>jacques.corbeil@crchul.ulaval.ca</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Infectious Diseases Research Center, CHUQ Research Center, 2705, boul. Laurier, Québec (Québec), G1V 4G2, Canada</aff>
<aff id="I2"><label>2</label>
Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada</aff>
<aff id="I3"><label>3</label>
Department of Computer Science and Software Engineering, Faculty of Science and Engineering, Laval University, 1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada</aff>
<aff id="I4"><label>4</label>
Department of Molecular Medicine, Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada</aff>
<pub-date pub-type="ppub"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>22</day>
<month>12</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<issue>12</issue>
<fpage>R122</fpage>
<lpage>R122</lpage>
<history><date date-type="received"><day>1</day>
<month>8</month>
<year>2012</year>
</date>
<date date-type="rev-recd"><day>19</day>
<month>11</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>22</day>
<month>12</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2012 Boisvert et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Boisvert et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://genomebiology.com/2012/13/12/R122"></self-uri>
<abstract><p>Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for <italic>de novo </italic>
assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at <ext-link ext-link-type="uri" xlink:href="http://denovoassembler.sf.net">http://denovoassembler.sf.net</ext-link>
.</p>
</abstract>
<kwd-group><kwd>metagenomics</kwd>
<kwd>message passing</kwd>
<kwd>scalability</kwd>
<kwd><italic>de novo </italic>
assembly</kwd>
<kwd>profiling</kwd>
<kwd>next-generation sequencing</kwd>
<kwd>parallel</kwd>
<kwd>distributed</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Canada</li>
</country>
</list>
<tree><country name="Canada"><noRegion><name sortKey="Boisvert, Sebastien" sort="Boisvert, Sebastien" uniqKey="Boisvert S" first="Sébastien" last="Boisvert">Sébastien Boisvert</name>
</noRegion>
<name sortKey="Boisvert, Sebastien" sort="Boisvert, Sebastien" uniqKey="Boisvert S" first="Sébastien" last="Boisvert">Sébastien Boisvert</name>
<name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name>
<name sortKey="Corbeil, Jacques" sort="Corbeil, Jacques" uniqKey="Corbeil J" first="Jacques" last="Corbeil">Jacques Corbeil</name>
<name sortKey="Godzaridis, Elenie" sort="Godzaridis, Elenie" uniqKey="Godzaridis E" first="Élénie" last="Godzaridis">Élénie Godzaridis</name>
<name sortKey="Laviolette, Francois" sort="Laviolette, Francois" uniqKey="Laviolette F" first="François" last="Laviolette">François Laviolette</name>
<name sortKey="Raymond, Frederic" sort="Raymond, Frederic" uniqKey="Raymond F" first="Frédéric" last="Raymond">Frédéric Raymond</name>
<name sortKey="Raymond, Frederic" sort="Raymond, Frederic" uniqKey="Raymond F" first="Frédéric" last="Raymond">Frédéric Raymond</name>
</country>
</tree>
</affiliations>
</record>
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