Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

J Dröge; I Gregor; A C McHardy

doi:10.1093/bioinformatics/btu745

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

Bioinformatics. 2015 Mar 15;31(6):817-24. doi: 10.1093/bioinformatics/btu745. Epub 2014 Nov 10.

Authors

J Dröge¹, I Gregor¹, A C McHardy²

Affiliations

¹ Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrücken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrücken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
² Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrücken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrücken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany Department for Algorithmic Bioinformatics, Heinrich Heine University, Universitätsstraße 1, 40225 Düsseldorf, Germany, Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, 66123 Saarbrücken, Germany and Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.

Abstract

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.

Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Bacteria / genetics*
Genomics / methods*
Metagenome*
Phylogeny*
Software