Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Sebastian Jaenicke; Christina Ander; Thomas Bekel; Regina Bisdorf; Marcus Dröge; Karl-Heinz Gartemann; Sebastian Jünemann; Olaf Kaiser; Lutz Krause; Felix Tille; Martha Zakrzewski; Alfred Pühler; Andreas Schlüter; Alexander Goesmann

doi:10.1371/journal.pone.0014519

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Peer-reviewed

Research Article

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Sebastian Jaenicke,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Christina Ander,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Thomas Bekel,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Regina Bisdorf,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Marcus Dröge,

Affiliation Roche Diagnostics GmbH, Penzberg, Germany
⨯
Karl-Heinz Gartemann,

Affiliation Department of Genetechnology/Microbiology, Bielefeld University, Bielefeld, Germany
⨯
Sebastian Jünemann,

Affiliations Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany, Department of Periodontology, University Hospital Münster, Münster, Germany
⨯
Olaf Kaiser,

Affiliation Roche Diagnostics GmbH, Penzberg, Germany
⨯
Lutz Krause,

Affiliation Division of Genetics and Population Health, Queensland Institute of Medical Research, Herston, Australia
⨯
Felix Tille,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Martha Zakrzewski,

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Alfred Pühler,

Affiliation Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Andreas Schlüter ,

Contributed equally to this work with: Andreas Schlüter, Alexander Goesmann

Affiliation Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯
Alexander Goesmann

Contributed equally to this work with: Andreas Schlüter, Alexander Goesmann

* E-mail: agoesman@CeBiTec.Uni-Bielefeld.DE

Affiliation Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
⨯

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Sebastian Jaenicke,
Christina Ander,
Thomas Bekel,
Regina Bisdorf,
Marcus Dröge,
Karl-Heinz Gartemann,
Sebastian Jünemann,
Olaf Kaiser,
Lutz Krause,
Felix Tille

Published: January 26, 2011
https://doi.org/10.1371/journal.pone.0014519

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Interesting

Posted by CarolinB on 29 Jan 2011 at 09:56 GMT

Also, the average GC content for different read lengths was analysed. Results showed that GC content and obtained read length clearly correlate for both GS FLX and the Titanium platform. The applied sequencing methods did not only generate reads with different average levels of GC content, but also both pyrosequencing platforms show a significant decline in GC content once the read length exceeds a certain value (Figure 1).
http://plosone.org/article/info:doi/10.1371/journal.pone.0014519#article1.body1.sec3.sec1.p1

Can confirm this observation for an in-house metagenome dataset (454 GS FLX). However, I have yet to implement the correction process as described by the authors - so I can't tell how many sequences would be affected by this. Losing almost 30% of the data doesn't sound too good..

No competing interests declared.

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Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

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Interesting

Posted by CarolinB on 29 Jan 2011 at 09:56 GMT