Good alternatives to BLAST style alignment are the dedicated aligners developed for next generation sequencing. Examples of these include Bowtie2, BWA, mrFAST. These aligners are extremely fast but often require an excessive amount of memory for storing the indexed database, especially when Ophiobolin A comprehensive sequence databases are used. A crucial step in all approaches is taxon assignment which is often carried out via various flavors of lowest common ancestor search within a taxonomic hierarchy. Briefly, alignment programs assign reads either to one taxon, or to several taxa, and in the latter case the lowest common taxonomic ancestor is reported. This principle is used in popular programs such as MEGAN, Perlapine Mothur and SOrt-ITEMS. The variety of computational approaches available suggests that there is a need for further computational improvements. For example, the need for dedicated tools for specific challenges is clear since most of the current software tools are developed for general research purposes. A further issue is that in research settings, qualitative and quantitative answers are not always clearly separated. For instance, the presence of E. coli reads in an output may be a safe indication for E. coli being present in an environmental sample, but the number of the identified reads is not necessarily a quantitative measure of the abundance of the species. Currently, only MetaPhlAn is considered a reliable quantitative indicator for species abundance in metagenome analyses. Finally, diagnostic settings pose a separate problem: here one has to precisely detect whether or not a pathogen is present above a certain threshold level, while the exact quantity is not necessarily important. In order to address the above issues we have developed Taxoner, a simple, parallelizable pipeline that allows one to align millions of reads against the full NT database of NCBI on a standard personal computer or laptop. Bowtie2 carries out the alignment and the output includes the alignments and the taxa assigned. Unlike most metagenome analysis programs, Taxoner allows identification and functional overview of the genes that received hits.