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. 2014 Sep 4;8(1):131–142. doi: 10.1111/1751-7915.12162

Table 3.

Bioinformatic parameters and databases used in the analysis of bar-coded pyrosequencing results

Step Parameter Targeted rDNA Gene
16S 18S
Preprocessing Length threshold 370 300
Number of ambiguities tolerated 0 0
Detection of proximal primer sequence Complete and perfect Complete and perfect
Detection of distal primer sequence No Perfect, but potentially incomplete
Clustering Chosen level of similarity (%) 95 95
Ignoring differences in homopolymer lengths Yes Yes
Filtering Chosen clustering similarity threshold 95 95
Used taxonomic database SILVA (r114) SILVA (r111)
Chosen taxonomic level Phylum Phylum
Similarity or confidence threshold (%) 90 85
Homogenization High-quality reads kept for each sample 2322 4378
Taxonomy Used taxonomic database SILVA (r114) SILVA (r111)
Method or tool of comparison usearch megablast
Similarity or confidence threshold (%) 80 80
Analysis Chosen level of similarity (%) 95 95
Ignoring differences in homopolymer lengths Yes Yes
Computation of a unifrac distance matrix Yes Yes