  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 us to identify the sequenced community members and to reconstruct
taxonomic bins with sequence data for the individual taxa. We describe an
algorithm and the accompanying software, taxator-tk, which performs taxonomic
sequence assignments by fast approximate determination of evolutionary
neighbors from sequence similarities. Taxator-tk was precise in its taxonomic
assignment across all ranks and taxa for a range of evolutionary distances and
for short sequences. In addition to the taxonomic binning of metagenomes, it is
well suited for profiling microbial communities from metagenome samples
becauseit 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 ten CPU cores and microbial RefSeq as the genomic reference data.
