454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes
Figure 4
Number of OTUs as a function of clustering level and filtering procedure.
The 454 pyrosequencing reads were processed with four different sequence filtering strategies, and the number of OTUs were calculated with and without singletons. (A) DNA-Hap454, (B) DNA-Prym454, (C) cDNA-Hap454, (D) cDNA-Prym454, (E) DNApool. Initial Filtering (IF): Initial filtering based on match with barcode and primer, and removal of reads with Ns and/or homopolymers >8 bp, and reads that are shorter than 365 bp. Quality Score (QS): requiring minimum average quality score 30 over a 50 bp moving window along the read, in addition to IF. PyroNoise (PN): the PyroNoise algorithm as implemented in mothur, with default settings. AmpliconNoise (AN): AmpliconNoise as implemented in Qiime v. 1.4.0, with default settings. The filtering strategies are described in the methods section.