Metagenomic analysis: the challenge of the data bonanza
Identifieur interne : 000350 ( Ncbi/Merge ); précédent : 000349; suivant : 000351Metagenomic analysis: the challenge of the data bonanza
Auteurs : Chris I. Hunter ; Alex Mitchell ; Philip Jones ; Craig Mcanulla ; Sebastien Pesseat ; Maxim Scheremetjew ; Sarah HunterSource :
- Briefings in Bioinformatics [ 1467-5463 ] ; 2012.
Abstract
Several thousand metagenomes have already been sequenced, and this number is set to grow rapidly in the forthcoming years as the uptake of high-throughput sequencing technologies continues. Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these challenges.
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DOI: 10.1093/bib/bbs020
PubMed: 22962339
PubMed Central: 3504930
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenomic analysis: the challenge of the data bonanza</title><author><name sortKey="Hunter, Chris I" sort="Hunter, Chris I" uniqKey="Hunter C" first="Chris I." last="Hunter">Chris I. Hunter</name></author><author><name sortKey="Mitchell, Alex" sort="Mitchell, Alex" uniqKey="Mitchell A" first="Alex" last="Mitchell">Alex Mitchell</name></author><author><name sortKey="Jones, Philip" sort="Jones, Philip" uniqKey="Jones P" first="Philip" last="Jones">Philip Jones</name></author><author><name sortKey="Mcanulla, Craig" sort="Mcanulla, Craig" uniqKey="Mcanulla C" first="Craig" last="Mcanulla">Craig Mcanulla</name></author><author><name sortKey="Pesseat, Sebastien" sort="Pesseat, Sebastien" uniqKey="Pesseat S" first="Sebastien" last="Pesseat">Sebastien Pesseat</name></author><author><name sortKey="Scheremetjew, Maxim" sort="Scheremetjew, Maxim" uniqKey="Scheremetjew M" first="Maxim" last="Scheremetjew">Maxim Scheremetjew</name></author><author><name sortKey="Hunter, Sarah" sort="Hunter, Sarah" uniqKey="Hunter S" first="Sarah" last="Hunter">Sarah Hunter</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22962339</idno><idno type="pmc">3504930</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504930</idno><idno type="RBID">PMC:3504930</idno><idno type="doi">10.1093/bib/bbs020</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000508</idno><idno type="wicri:Area/Pmc/Curation">000508</idno><idno type="wicri:Area/Pmc/Checkpoint">000394</idno><idno type="wicri:Area/Ncbi/Merge">000350</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metagenomic analysis: the challenge of the data bonanza</title><author><name sortKey="Hunter, Chris I" sort="Hunter, Chris I" uniqKey="Hunter C" first="Chris I." last="Hunter">Chris I. Hunter</name></author><author><name sortKey="Mitchell, Alex" sort="Mitchell, Alex" uniqKey="Mitchell A" first="Alex" last="Mitchell">Alex Mitchell</name></author><author><name sortKey="Jones, Philip" sort="Jones, Philip" uniqKey="Jones P" first="Philip" last="Jones">Philip Jones</name></author><author><name sortKey="Mcanulla, Craig" sort="Mcanulla, Craig" uniqKey="Mcanulla C" first="Craig" last="Mcanulla">Craig Mcanulla</name></author><author><name sortKey="Pesseat, Sebastien" sort="Pesseat, Sebastien" uniqKey="Pesseat S" first="Sebastien" last="Pesseat">Sebastien Pesseat</name></author><author><name sortKey="Scheremetjew, Maxim" sort="Scheremetjew, Maxim" uniqKey="Scheremetjew M" first="Maxim" last="Scheremetjew">Maxim Scheremetjew</name></author><author><name sortKey="Hunter, Sarah" sort="Hunter, Sarah" uniqKey="Hunter S" first="Sarah" last="Hunter">Sarah Hunter</name></author></analytic><series><title level="j">Briefings in Bioinformatics</title><idno type="ISSN">1467-5463</idno><idno type="eISSN">1477-4054</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Several thousand metagenomes have already been sequenced, and this number is set to grow rapidly in the forthcoming years as the uptake of high-throughput sequencing technologies continues. Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these challenges.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wooley, Jc" uniqKey="Wooley J">JC Wooley</name></author><author><name sortKey="Godzik, A" uniqKey="Godzik A">A Godzik</name></author><author><name sortKey="Friedberg, I" uniqKey="Friedberg I">I Friedberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J Gilbert</name></author><author><name sortKey="Dupont, C" uniqKey="Dupont C">C Dupont</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hildebrandt, A" uniqKey="Hildebrandt A">A Hildebrandt</name></author><author><name sortKey="Lacorte, S" uniqKey="Lacorte S">S Lacorte</name></author><author><name sortKey="Barcel, D" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Brief Bioinform</journal-id><journal-id journal-id-type="iso-abbrev">Brief. Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">bib</journal-id><journal-id journal-id-type="hwp">bib</journal-id><journal-title-group><journal-title>Briefings in Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1467-5463</issn><issn pub-type="epub">1477-4054</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22962339</article-id><article-id pub-id-type="pmc">3504930</article-id><article-id pub-id-type="doi">10.1093/bib/bbs020</article-id><article-id pub-id-type="publisher-id">bbs020</article-id><article-categories><subj-group subj-group-type="heading"><subject>Papers</subject></subj-group></article-categories><title-group><article-title>Metagenomic analysis: the challenge of the data bonanza</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Hunter</surname><given-names>Chris I.</given-names></name><xref ref-type="bio" rid="d34e36">*</xref></contrib><contrib contrib-type="author"><name><surname>Mitchell</surname><given-names>Alex</given-names></name><xref ref-type="bio" rid="d34e49">*</xref></contrib><contrib contrib-type="author"><name><surname>Jones</surname><given-names>Philip</given-names></name><xref ref-type="bio" rid="d34e62">*</xref></contrib><contrib contrib-type="author"><name><surname>McAnulla</surname><given-names>Craig</given-names></name><xref ref-type="bio" rid="d34e75">*</xref></contrib><contrib contrib-type="author"><name><surname>Pesseat</surname><given-names>Sebastien</given-names></name><xref ref-type="bio" rid="d34e88">*</xref></contrib><contrib contrib-type="author"><name><surname>Scheremetjew</surname><given-names>Maxim</given-names></name><xref ref-type="bio" rid="d34e101">*</xref></contrib><contrib contrib-type="author"><name><surname>Hunter</surname><given-names>Sarah</given-names></name><xref ref-type="bio" rid="d34e114">*</xref></contrib></contrib-group><author-notes><corresp>Corresponding author. Chris I. Hunter, EMBL Outstation European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK. Tel.: <phone>+44 (0) 1223 494 444</phone>; Fax: <fax>+44 (0)1223 494 468</fax>; E-mail: <email>chrish@ebi.ac.uk</email></corresp></author-notes><pub-date pub-type="ppub"><month>11</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>7</day><month>9</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>7</day><month>9</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>13</volume><issue>6</issue><issue-title>Special Issue: Bioinformatics approaches and tools for metagenomic analysis</issue-title><fpage>743</fpage><lpage>746</lpage><history><date date-type="received"><day>4</day><month>11</month><year>2011</year></date><date date-type="accepted"><day>27</day><month>1</month><year>2012</year></date></history><permissions><copyright-statement>© The Author 2012. Published by Oxford University Press.</copyright-statement><copyright-year>2012</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>Several thousand metagenomes have already been sequenced, and this number is set to grow rapidly in the forthcoming years as the uptake of high-throughput sequencing technologies continues. Hand-in-hand with this data bonanza comes the computationally overwhelming task of analysis. Herein, we describe some of the bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issues they face and the steps that could be taken to help overcome these challenges.</p></abstract><kwd-group><kwd>metagenomics</kwd><kwd>next-generation sequencing (NGS)</kwd><kwd>high-throughput sequencing (HTS)</kwd><kwd>functional analysis</kwd><kwd>environmental bioinformatics</kwd></kwd-group><counts><page-count count="4"></page-count></counts></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Hunter, Chris I" sort="Hunter, Chris I" uniqKey="Hunter C" first="Chris I." last="Hunter">Chris I. Hunter</name><name sortKey="Hunter, Sarah" sort="Hunter, Sarah" uniqKey="Hunter S" first="Sarah" last="Hunter">Sarah Hunter</name><name sortKey="Jones, Philip" sort="Jones, Philip" uniqKey="Jones P" first="Philip" last="Jones">Philip Jones</name><name sortKey="Mcanulla, Craig" sort="Mcanulla, Craig" uniqKey="Mcanulla C" first="Craig" last="Mcanulla">Craig Mcanulla</name><name sortKey="Mitchell, Alex" sort="Mitchell, Alex" uniqKey="Mitchell A" first="Alex" last="Mitchell">Alex Mitchell</name><name sortKey="Pesseat, Sebastien" sort="Pesseat, Sebastien" uniqKey="Pesseat S" first="Sebastien" last="Pesseat">Sebastien Pesseat</name><name sortKey="Scheremetjew, Maxim" sort="Scheremetjew, Maxim" uniqKey="Scheremetjew M" first="Maxim" last="Scheremetjew">Maxim Scheremetjew</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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