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Metagenomics characterizes microbial communities by random shotgun sequencingof DNA isolated directly from an environment of interest. An essential step incomputational metagenome analysis is taxonomic sequence assignment, whichallows us to identify the sequenced community members and to reconstructtaxonomic bins with sequence data for the individual taxa. We describe analgorithm and the accompanying software, taxator-tk, which performs taxonomicsequence assignments by fast approximate determination of evolutionaryneighbors from sequence similarities. Taxator-tk was precise in its taxonomicassignment across all ranks and taxa for a range of evolutionary distances andfor short sequences. In addition to the taxonomic binning of metagenomes, it iswell suited for profiling microbial communities from metagenome samplesbecauseit identifies bacterial, archaeal and eukaryotic community memberswithout being affected by varying primer binding strengths, as in marker geneamplification, or copy number variations of marker genes across different taxa.Taxator-tk has an efficient, parallelized implementation that allows theassignment of 6 Gb of sequence data per day on a standard multiprocessor systemwith ten CPU cores and microbial RefSeq as the genomic reference data.

Taxator-tk: Fast and Precise Taxonomic Assignment of Metagenomes by Approximating Evolutionary Neighborhoods