biostudies-literatureUnknown6Nearing JTNSERC Discovery GrantNSERC Alexander Graham Bell Canada Graduate ScholarshipTerry Fox Research Institute (TFRI)High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity threshold to avoid sequencing errors generating spurious taxonomic units. However, there have been numerous bioinformatic packages recently released that attempt to correct sequencing errors to determine real biological sequences at single nucleotide resolution by generating amplicon sequence variants (ASVs). As more researchers begin to use high resolution ASVs, there is a need for an in-depth and unbiased comparison of these novel "denoising" pipelines. In this study, we conduct a thorough comparison of three of the most widely-used denoising packages (DADAPeerJe5364https://www.ebi.ac.uk/biostudies/studies/S-EPMC6087418biostudies-literatureDenoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches.PMC6087418Nearing JTDouglas GMLangille MGIComeau AMfalseDenoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches.High-depth sequencing of universal marker genes such as the 16S rRNA gene is a common strategy to profile microbial communities. Traditionally, sequence reads are clustered into operational taxonomic units (OTUs) at a defined identity threshold to avoid sequencing errors generating spurious taxonomic units. However, there have been numerous bioinformatic packages recently released that attempt to correct sequencing errors to determine real biological sequences at single nucleotide resolution by generating amplicon sequence variants (ASVs). As more researchers begin to use high resolution ASVs, there is a need for an in-depth and unbiased comparison of these novel "denoising" pipelines. In this study, we conduct a thorough comparison of three of the most widely-used denoising packages (DADA2018-01-01T00:00:00Z20182026-05-02T09:47:04.672Z2019-03-26T23:52:05ZS-EPMC60874183012370510.7717/peerj.5364