The analysis of the huge amount of generated sequence data as well as pyrosequencing noise and chimeric sequences originating from PCR amplification pose a considerable challenge to the individual researcher in doing microbiome studies. The unbiased knowledge about microbial community composition and -structure as well as the interactions with the human host microbiome can give important insights into its role in human health and disease. Here we introduce SnoWMAn, the high-throughput microbiome analysis pipeline and additionally investigate the effects of sequencing noise on non denoised and data denoised using two different approaches.