Abstract

We developed a fast method for denoising pyrosequencing for community 16S rRNA analysis. We observe a 2–4 fold reduction in the number of observed OTUs (operational taxonomic units) comparing denoised with non-denoised data. ~50,000 sequences can be denoised on a laptop within an hour, two orders of magnitude faster than published techniques. We demonstrate the effects of denoising on alpha and beta diversity of large 16S rRNA datasets. Keywords next generation DNA sequencing; ribosomal RNA; community sequence analysis; microbial ecology; denoising Pyrosequencing1 has revolutionized microbial community analysis by allowing the simultaneous assessment of hundreds of microbial communities in multiplex with sufficient depth to resolve meaningful biological patterns2. These techniques have been used to gain striking new insight into microbial processes on scales ranging from continents3 to within an individual’s body4. Although powerful new analysis tools such as GAST5, Mothur6, and QIIME7 greatly