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MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman

Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause, Daniel H. Huson
doi: https://doi.org/10.1101/050559
Alexander Herbig
1Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72072 Tübingen, Germany.
2Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.
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  • For correspondence: herbig@shh.mpg.de krause@shh.mpg.de daniel.huson@uni-tuebingen.de
Frank Maixner
3Institute for Mummies and the Iceman, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy.
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Kirsten I. Bos
1Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72072 Tübingen, Germany.
2Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.
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Albert Zink
3Institute for Mummies and the Iceman, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, 39100 Bolzano, Italy.
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Johannes Krause
1Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72072 Tübingen, Germany.
2Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.
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  • For correspondence: herbig@shh.mpg.de krause@shh.mpg.de daniel.huson@uni-tuebingen.de
Daniel H. Huson
4Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
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  • For correspondence: herbig@shh.mpg.de krause@shh.mpg.de daniel.huson@uni-tuebingen.de
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Abstract

Modern next generation sequencing technologies produce vast amounts of data in the context of large-scale metagenomic studies, in which complex microbial communities can be reconstructed to an unprecedented level of detail. Most prominent examples are human microbiome studies that correlate the bacterial taxonomic profile with specific physiological conditions or diseases.

In order to perform these analyses high-throughput computational tools are needed that are able to process these data within a short time while preserving a high level of sensitivity and specificity.

Here we present MALT (MEGAN ALignment Tool) a program for the ultrafast alignment and analysis of metagenomic DNA sequencing data. MALT processes hundreds of millions of sequencing reads within only a few hours. In addition to the alignment procedure MALT implements a taxonomic binning algorithm that is able to specifically assign reads to bacterial species. Its tight integration with the interactive metagenomic analysis software MEGAN allows for visualization and further analyses of results.

We demonstrate MALT by its application to the metagenomic analysis of two ancient microbiomes from oral cavity and lung samples of the 5,300-year-old Tyrolean Iceman. Despite the strong environmental background, MALT is able to pick up the weak signal of the original microbiomes and identifies multiple species that are typical representatives of the respective host environment.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted April 27, 2016.
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MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman
Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause, Daniel H. Huson
bioRxiv 050559; doi: https://doi.org/10.1101/050559
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MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman
Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause, Daniel H. Huson
bioRxiv 050559; doi: https://doi.org/10.1101/050559

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