Kraken: ultrafast metagenomic sequence classification using exact alignments
Identifieur interne : 001049 ( Pmc/Checkpoint ); précédent : 001048; suivant : 001050Kraken: ultrafast metagenomic sequence classification using exact alignments
Auteurs : Derrick E. Wood [États-Unis] ; Steven L. Salzberg [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2014.
Abstract
Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of
Url:
DOI: 10.1186/gb-2014-15-3-r46
PubMed: 24580807
PubMed Central: 4053813
Affiliations:
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Kraken: ultrafast metagenomic sequence classification using exact alignments</title>
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<front><div type="abstract" xml:lang="en"><p>Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of <italic>k</italic>
-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at <ext-link ext-link-type="uri" xlink:href="http://ccb.jhu.edu/software/kraken/">http://ccb.jhu.edu/software/kraken/</ext-link>
.</p>
</div>
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<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Venter, C" uniqKey="Venter C">C Venter</name>
</author>
<author><name sortKey="Remington, K" uniqKey="Remington K">K Remington</name>
</author>
<author><name sortKey="Heidelberg, J" uniqKey="Heidelberg J">J Heidelberg</name>
</author>
<author><name sortKey="Halpern, A" uniqKey="Halpern A">A Halpern</name>
</author>
<author><name sortKey="Rusch, D" uniqKey="Rusch D">D Rusch</name>
</author>
<author><name sortKey="Eisen, J" uniqKey="Eisen J">J Eisen</name>
</author>
<author><name sortKey="Wu, D" uniqKey="Wu D">D Wu</name>
</author>
<author><name sortKey="Paulsen, I" uniqKey="Paulsen I">I Paulsen</name>
</author>
<author><name sortKey="Nelson, K" uniqKey="Nelson K">K Nelson</name>
</author>
<author><name sortKey="Nelson, W" uniqKey="Nelson W">W Nelson</name>
</author>
<author><name sortKey="Fouts, D" uniqKey="Fouts D">D Fouts</name>
</author>
<author><name sortKey="Levy, S" uniqKey="Levy S">S Levy</name>
</author>
<author><name sortKey="Knap, A" uniqKey="Knap A">A Knap</name>
</author>
<author><name sortKey="Lomas, M" uniqKey="Lomas M">M Lomas</name>
</author>
<author><name sortKey="Nealson, K" uniqKey="Nealson K">K Nealson</name>
</author>
<author><name sortKey="White, O" uniqKey="White O">O White</name>
</author>
<author><name sortKey="Peterson, J" uniqKey="Peterson J">J Peterson</name>
</author>
<author><name sortKey="Hoffman, J" uniqKey="Hoffman J">J Hoffman</name>
</author>
<author><name sortKey="Parsons, R" uniqKey="Parsons R">R Parsons</name>
</author>
<author><name sortKey="Baden Tillson, H" uniqKey="Baden Tillson H">H Baden-Tillson</name>
</author>
<author><name sortKey="Pfannkoch, C" uniqKey="Pfannkoch C">C Pfannkoch</name>
</author>
<author><name sortKey="Rogers, Y H" uniqKey="Rogers Y">Y-H Rogers</name>
</author>
<author><name sortKey="Smith, H" uniqKey="Smith H">H Smith</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Tyson, G" uniqKey="Tyson G">G Tyson</name>
</author>
<author><name sortKey="Chapman, J" uniqKey="Chapman J">J Chapman</name>
</author>
<author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
<author><name sortKey="Allen, E" uniqKey="Allen E">E Allen</name>
</author>
<author><name sortKey="Ram, R" uniqKey="Ram R">R Ram</name>
</author>
<author><name sortKey="Richardson, P" uniqKey="Richardson P">P Richardson</name>
</author>
<author><name sortKey="Solovyev, V" uniqKey="Solovyev V">V Solovyev</name>
</author>
<author><name sortKey="Rubin, E" uniqKey="Rubin E">E Rubin</name>
</author>
<author><name sortKey="Rokhsar, D" uniqKey="Rokhsar D">D Rokhsar</name>
</author>
<author><name sortKey="Banfield, J" uniqKey="Banfield J">J Banfield</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
<author><name sortKey="Gevers, D" uniqKey="Gevers D">D Gevers</name>
</author>
<author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name>
</author>
<author><name sortKey="Abubucker, S" uniqKey="Abubucker S">S Abubucker</name>
</author>
<author><name sortKey="Badger, Jh" uniqKey="Badger J">JH Badger</name>
</author>
<author><name sortKey="Chinwalla, At" uniqKey="Chinwalla A">AT Chinwalla</name>
</author>
<author><name sortKey="Creasy, Hh" uniqKey="Creasy H">HH Creasy</name>
</author>
<author><name sortKey="Earl, Am" uniqKey="Earl A">AM Earl</name>
</author>
<author><name sortKey="Fitzgerald, Mg" uniqKey="Fitzgerald M">MG FitzGerald</name>
</author>
<author><name sortKey="Fulton, Rs" uniqKey="Fulton R">RS Fulton</name>
</author>
<author><name sortKey="Giglio, Mg" uniqKey="Giglio M">MG Giglio</name>
</author>
<author><name sortKey="Hallsworth Pepin, K" uniqKey="Hallsworth Pepin K">K Hallsworth-Pepin</name>
</author>
<author><name sortKey="Lobos, Ea" uniqKey="Lobos E">EA Lobos</name>
</author>
<author><name sortKey="Madupu, R" uniqKey="Madupu R">R Madupu</name>
</author>
<author><name sortKey="Magrini, V" uniqKey="Magrini V">V Magrini</name>
</author>
<author><name sortKey="Martin, Jc" uniqKey="Martin J">JC Martin</name>
</author>
<author><name sortKey="Mitreva, M" uniqKey="Mitreva M">M Mitreva</name>
</author>
<author><name sortKey="Muzny, Dm" uniqKey="Muzny D">DM Muzny</name>
</author>
<author><name sortKey="Sodergren, Ej" uniqKey="Sodergren E">EJ Sodergren</name>
</author>
<author><name sortKey="Versalovic, J" uniqKey="Versalovic J">J Versalovic</name>
</author>
<author><name sortKey="Wollam, Am" uniqKey="Wollam A">AM Wollam</name>
</author>
<author><name sortKey="Worley, Kc" uniqKey="Worley K">KC Worley</name>
</author>
<author><name sortKey="Wortman, Jr" uniqKey="Wortman J">JR Wortman</name>
</author>
<author><name sortKey="Young, Sk" uniqKey="Young S">SK Young</name>
</author>
<author><name sortKey="Zeng, Q" uniqKey="Zeng Q">Q Zeng</name>
</author>
<author><name sortKey="Aagaard, Km" uniqKey="Aagaard K">KM Aagaard</name>
</author>
<author><name sortKey="Abolude, Oo" uniqKey="Abolude O">OO Abolude</name>
</author>
<author><name sortKey="Allen Vercoe, E" uniqKey="Allen Vercoe E">E Allen-Vercoe</name>
</author>
<author><name sortKey="Alm, Ej" uniqKey="Alm E">EJ Alm</name>
</author>
<author><name sortKey="Alvarado, L" uniqKey="Alvarado L">L Alvarado</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Altschul, S" uniqKey="Altschul S">S Altschul</name>
</author>
<author><name sortKey="Gish, W" uniqKey="Gish W">W Gish</name>
</author>
<author><name sortKey="Miller, W" uniqKey="Miller W">W Miller</name>
</author>
<author><name sortKey="Myers, E" uniqKey="Myers E">E Myers</name>
</author>
<author><name sortKey="Lipman, D" uniqKey="Lipman D">D Lipman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, D" uniqKey="Huson D">D Huson</name>
</author>
<author><name sortKey="Auch, A" uniqKey="Auch A">A Auch</name>
</author>
<author><name sortKey="Qi, J" uniqKey="Qi J">J Qi</name>
</author>
<author><name sortKey="Schuster, S" uniqKey="Schuster S">S Schuster</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Brady, A" uniqKey="Brady A">A Brady</name>
</author>
<author><name sortKey="Salzberg, S" uniqKey="Salzberg S">S Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rosen, G" uniqKey="Rosen G">G Rosen</name>
</author>
<author><name sortKey="Garbarine, E" uniqKey="Garbarine E">E Garbarine</name>
</author>
<author><name sortKey="Caseiro, D" uniqKey="Caseiro D">D Caseiro</name>
</author>
<author><name sortKey="Polikar, R" uniqKey="Polikar R">R Polikar</name>
</author>
<author><name sortKey="Sokhansanj, B" uniqKey="Sokhansanj B">B Sokhansanj</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name>
</author>
<author><name sortKey="Gibbons, T" uniqKey="Gibbons T">T Gibbons</name>
</author>
<author><name sortKey="Ghodsi, M" uniqKey="Ghodsi M">M Ghodsi</name>
</author>
<author><name sortKey="Treangen, T" uniqKey="Treangen T">T Treangen</name>
</author>
<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Segata, N" uniqKey="Segata N">N Segata</name>
</author>
<author><name sortKey="Waldron, L" uniqKey="Waldron L">L Waldron</name>
</author>
<author><name sortKey="Ballarini, A" uniqKey="Ballarini A">A Ballarini</name>
</author>
<author><name sortKey="Narasimhan, V" uniqKey="Narasimhan V">V Narasimhan</name>
</author>
<author><name sortKey="Jousson, O" uniqKey="Jousson O">O Jousson</name>
</author>
<author><name sortKey="Huttenhower, C" uniqKey="Huttenhower C">C Huttenhower</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Treangen, T" uniqKey="Treangen T">T Treangen</name>
</author>
<author><name sortKey="Koren, S" uniqKey="Koren S">S Koren</name>
</author>
<author><name sortKey="Sommer, D" uniqKey="Sommer D">D Sommer</name>
</author>
<author><name sortKey="Liu, B" uniqKey="Liu B">B Liu</name>
</author>
<author><name sortKey="Astrovskaya, I" uniqKey="Astrovskaya I">I Astrovskaya</name>
</author>
<author><name sortKey="Ondov, B" uniqKey="Ondov B">B Ondov</name>
</author>
<author><name sortKey="Darling, A" uniqKey="Darling A">A Darling</name>
</author>
<author><name sortKey="Phillippy, A" uniqKey="Phillippy A">A Phillippy</name>
</author>
<author><name sortKey="Pop, M" uniqKey="Pop M">M Pop</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ames, Sk" uniqKey="Ames S">SK Ames</name>
</author>
<author><name sortKey="Hysom, Da" uniqKey="Hysom D">DA Hysom</name>
</author>
<author><name sortKey="Gardner, Sn" uniqKey="Gardner S">SN Gardner</name>
</author>
<author><name sortKey="Lloyd, Gs" uniqKey="Lloyd G">GS Lloyd</name>
</author>
<author><name sortKey="Gokhale, Mb" uniqKey="Gokhale M">MB Gokhale</name>
</author>
<author><name sortKey="Allen, Je" uniqKey="Allen J">JE Allen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kindblom, C" uniqKey="Kindblom C">C Kindblom</name>
</author>
<author><name sortKey="Davies, Jr" uniqKey="Davies J">JR Davies</name>
</author>
<author><name sortKey="Herzberg, Mc" uniqKey="Herzberg M">MC Herzberg</name>
</author>
<author><name sortKey="Svens Ter, G" uniqKey="Svens Ter G">G Svensäter</name>
</author>
<author><name sortKey="Wickstrom, C" uniqKey="Wickstrom C">C Wickström</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Foweraker, Je" uniqKey="Foweraker J">JE Foweraker</name>
</author>
<author><name sortKey="Cooke, Nj" uniqKey="Cooke N">NJ Cooke</name>
</author>
<author><name sortKey="Hawkey, Pm" uniqKey="Hawkey P">PM Hawkey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kononen, E" uniqKey="Kononen E">E Könönen</name>
</author>
<author><name sortKey="Saarela, M" uniqKey="Saarela M">M Saarela</name>
</author>
<author><name sortKey="Karjalainen, J" uniqKey="Karjalainen J">J Karjalainen</name>
</author>
<author><name sortKey="Jousimies Somer, H" uniqKey="Jousimies Somer H">H Jousimies-Somer</name>
</author>
<author><name sortKey="Alaluusua, S" uniqKey="Alaluusua S">S Alaluusua</name>
</author>
<author><name sortKey="Asikainen, S" uniqKey="Asikainen S">S Asikainen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Camacho, C" uniqKey="Camacho C">C Camacho</name>
</author>
<author><name sortKey="Coulouris, G" uniqKey="Coulouris G">G Coulouris</name>
</author>
<author><name sortKey="Avagyan, V" uniqKey="Avagyan V">V Avagyan</name>
</author>
<author><name sortKey="Ma, N" uniqKey="Ma N">N Ma</name>
</author>
<author><name sortKey="Papadopoulos, J" uniqKey="Papadopoulos J">J Papadopoulos</name>
</author>
<author><name sortKey="Bealer, K" uniqKey="Bealer K">K Bealer</name>
</author>
<author><name sortKey="Madden, T" uniqKey="Madden T">T Madden</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zimin, Av" uniqKey="Zimin A">AV Zimin</name>
</author>
<author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name>
</author>
<author><name sortKey="Puiu, D" uniqKey="Puiu D">D Puiu</name>
</author>
<author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
<author><name sortKey="Yorke, Ja" uniqKey="Yorke J">JA Yorke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Pruitt, Kd" uniqKey="Pruitt K">KD Pruitt</name>
</author>
<author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name>
</author>
<author><name sortKey="Brown, Gr" uniqKey="Brown G">GR Brown</name>
</author>
<author><name sortKey="Maglott, Dr" uniqKey="Maglott D">DR Maglott</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Marcais, G" uniqKey="Marcais G">G Marçais</name>
</author>
<author><name sortKey="Kingsford, C" uniqKey="Kingsford C">C Kingsford</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roberts, M" uniqKey="Roberts M">M Roberts</name>
</author>
<author><name sortKey="Hayes, W" uniqKey="Hayes W">W Hayes</name>
</author>
<author><name sortKey="Hunt, B" uniqKey="Hunt B">B Hunt</name>
</author>
<author><name sortKey="Mount, S" uniqKey="Mount S">S Mount</name>
</author>
<author><name sortKey="Yorke, J" uniqKey="Yorke J">J Yorke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Magoc, T" uniqKey="Magoc T">T Magoc</name>
</author>
<author><name sortKey="Pabinger, S" uniqKey="Pabinger S">S Pabinger</name>
</author>
<author><name sortKey="Canzar, S" uniqKey="Canzar S">S Canzar</name>
</author>
<author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name>
</author>
<author><name sortKey="Su, Q" uniqKey="Su Q">Q Su</name>
</author>
<author><name sortKey="Puiu, D" uniqKey="Puiu D">D Puiu</name>
</author>
<author><name sortKey="Tallon, Lj" uniqKey="Tallon L">LJ Tallon</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Shapiro, H" uniqKey="Shapiro H">H Shapiro</name>
</author>
<author><name sortKey="Goltsman, E" uniqKey="Goltsman E">E Goltsman</name>
</author>
<author><name sortKey="Mchardy, A" uniqKey="Mchardy A">A McHardy</name>
</author>
<author><name sortKey="Rigoutsos, I" uniqKey="Rigoutsos I">I Rigoutsos</name>
</author>
<author><name sortKey="Salamov, A" uniqKey="Salamov A">A Salamov</name>
</author>
<author><name sortKey="Korzeniewski, F" uniqKey="Korzeniewski F">F Korzeniewski</name>
</author>
<author><name sortKey="Land, M" uniqKey="Land M">M Land</name>
</author>
<author><name sortKey="Lapidus, A" uniqKey="Lapidus A">A Lapidus</name>
</author>
<author><name sortKey="Grigoriev, I" uniqKey="Grigoriev I">I Grigoriev</name>
</author>
<author><name sortKey="Richardson, P" uniqKey="Richardson P">P Richardson</name>
</author>
<author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
<author><name sortKey="Kyrpides, N" uniqKey="Kyrpides N">N Kyrpides</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ondov, B" uniqKey="Ondov B">B Ondov</name>
</author>
<author><name sortKey="Bergman, N" uniqKey="Bergman N">N Bergman</name>
</author>
<author><name sortKey="Phillippy, A" uniqKey="Phillippy A">A Phillippy</name>
</author>
</analytic>
</biblStruct>
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<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">24580807</article-id>
<article-id pub-id-type="pmc">4053813</article-id>
<article-id pub-id-type="publisher-id">gb-2014-15-3-r46</article-id>
<article-id pub-id-type="doi">10.1186/gb-2014-15-3-r46</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Method</subject>
</subj-group>
</article-categories>
<title-group><article-title>Kraken: ultrafast metagenomic sequence classification using exact alignments</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Wood</surname>
<given-names>Derrick E</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>dwood@cs.umd.edu</email>
</contrib>
<contrib contrib-type="author" id="A2"><name><surname>Salzberg</surname>
<given-names>Steven L</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>salzberg@jhu.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA</aff>
<aff id="I2"><label>2</label>
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</aff>
<aff id="I3"><label>3</label>
Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA</aff>
<pub-date pub-type="ppub"><year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>3</day>
<month>3</month>
<year>2014</year>
</pub-date>
<volume>15</volume>
<issue>3</issue>
<fpage>R46</fpage>
<lpage>R46</lpage>
<history><date date-type="received"><day>17</day>
<month>11</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>3</day>
<month>3</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Wood and Salzberg; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>Wood and Salzberg; 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/2014/15/3/R46"></self-uri>
<abstract><p>Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of <italic>k</italic>
-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at <ext-link ext-link-type="uri" xlink:href="http://ccb.jhu.edu/software/kraken/">http://ccb.jhu.edu/software/kraken/</ext-link>
.</p>
</abstract>
<kwd-group><kwd>metagenomics</kwd>
<kwd>sequence classification</kwd>
<kwd>sequence alignment</kwd>
<kwd>next-generation sequencing</kwd>
<kwd>microbiome</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Maryland</li>
</region>
<settlement><li>College Park (Maryland)</li>
</settlement>
<orgName><li>Université du Maryland</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Maryland"><name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name>
</region>
<name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name>
<name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name>
<name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name>
</country>
</tree>
</affiliations>
</record>
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