Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys (original) (raw)
Figure 2
The RDS processing method replicates de novo OTU clustering better than reference-based clustering.
The correlation between OTU clustering methods is shown by plotting the number of raw (a) and filtered (b) OTUs observed when using de novo OTU clustering versus reference or the RDS method. The reference-based OTU clustering results are depicted with squares while the RDS OTU clustering results are depicted with circles. Open markers indicate samples where the Greengenes 2012 reference was used while closed markers indicate samples where the Greengenes 2013 reference was used. De novo results are depicted as gray diamonds. Linear regression lines are shown for the reference and RDS datasets, with dash lines fitted to datasets processed using the Greengenes 2012–10 reference and solid lines fitted to datasets processed using the Greengenes 2013–08 reference.