Thumbnail Image
Publication

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

Dröge, J
; 
Gregor, I
; 
McHardy, A C
Citations
Altmetric:
Advisors
Editors
Other Contributors
Issue Date
2014-11-10
Submitted date
Show all metadata
Files
Thumbnail Image
Open Access publication
Adobe PDF, 919.75 KB
Thumbnail Image
Supplementary methods
Adobe PDF, 6.98 MB
Other Titles
Abstract
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.
Citation
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. 2014: Bioinformatics
Affiliation
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.
Publisher
Journal
Bioinformatics (Oxford, England)
URI
http://hdl.handle.net/10033/337182
DOI
10.1093/bioinformatics/btu745
PubMed ID
25388150
PubMed Central ID
Additional Links
Embedded video
Type
Article
Language
Description
Series/Report no.
ISSN
1367-4811
EISSN
ISBN
ISMN
Gov't Doc #
Sponsors
License
Collections
publications of the research group bioinformatics in infection research ([BRICS] BIFO)