Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Colin F. Davenport; Jens Neugebauer; Nils Beckmann; Benedikt Friedrich; Burim Kameri; Svea Kokott; Malte Paetow; Björn Siekmann; Matthias Wieding-Drewes; Markus Wienhöfer; Stefan Wolf; Burkhard Tümmler; Volker Ahlers; Frauke Sprengel

doi:10.1371/journal.pone.0041224

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Open Access

Peer-reviewed

Research Article

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Colin F. Davenport ,

* E-mail: davenport.colin@mh-hannover.de

Affiliation Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
⨯
Jens Neugebauer,

Affiliation Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
⨯
Nils Beckmann,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Benedikt Friedrich,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Burim Kameri,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Svea Kokott,

Affiliation Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
⨯
Malte Paetow,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Björn Siekmann,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Matthias Wieding-Drewes,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Markus Wienhöfer,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Stefan Wolf,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Burkhard Tümmler,

Affiliation Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Lower Saxony, Germany
⨯
Volker Ahlers,

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯
Frauke Sprengel

Affiliation Department of Computer Science, University of Applied Sciences and Arts, Hannover, Hannover, Lower Saxony, Germany
⨯

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Colin F. Davenport,
Jens Neugebauer,
Nils Beckmann,
Benedikt Friedrich,
Burim Kameri,
Svea Kokott,
Malte Paetow,
Björn Siekmann,
Matthias Wieding-Drewes,
Markus Wienhöfer

Published: August 21, 2012
https://doi.org/10.1371/journal.pone.0041224

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Comparison with MetaPhlAn

Posted by turnersd on 03 Sep 2012 at 14:50 GMT

It would be nice to see a comparison with MetaPhlAn (http://www.nature.com/nme...) - another recently introduced tool for species identification and binning from metagenomics data. MetaPhlAn also outperformed existing methods like MEGAN, Phymm/PhymmBL, etc.

No competing interests declared.

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Metagenomics
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BLAST algorithm
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Sequence alignment
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Genome sequencing
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Shotgun sequencing
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Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

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Comparison with MetaPhlAn

Posted by turnersd on 03 Sep 2012 at 14:50 GMT