NG-Tax is an improved pipeline for 16S rRNA gene amplicon sequencing data. Several novel steps ensure improved robustness against errors associated with technical aspects of these studies, such as PCR protocols, choice of 16S rRNA gene variable region and variable rates of sequencing error. The commonly reported problems such as many un- or poorly classified OTUs, inflated richness and diversity, taxonomic profiles that do not match the expected ones, region dependent taxonomic classification and results being highly dependent on minor changes in the experimental setup have been tackled with NG-Tax.