Additional file 2.
Assessment of mapping performances with pyrosequencing datasets denoised without (0–500 bp) and with (300–500 bp) minimal read length cutoff. Examples are given for the groundwater sample GRW01, the flocculent activated sludge sample FLS01 and the aerobic granular sludge sample AGS01. After denoising with the one or the other method, each dataset was mapped against a reference database with MG-RAST . No cutoff was set for e-value, minimum identity and minimum alignment length. After having observed that between 35-45% of the sequences were unassigned with Greengenes, RDP – the Ribosomal Database Project  was used as reference database for this assessment (only 4% unassigned sequences). Correlations between bacterial community profiles obtained with both denoising methods and both reference databases were analyzed with STAMP .
Format: PDF Size: 375KB Download file
This file can be viewed with: Adobe Acrobat Reader
Weissbrodt et al. BMC Microbiology 2012 12:306 doi:10.1186/1471-2180-12-306