Table 1. Overview of the guidelines to tune up the quality filtering parameters (adapted from Bokulich et al. (2013)).

Dataset characteristics	q	p	r	Results
Majority of high-quality, full-length sequences	increase	increase	-	Retrieving full-length sequences with low error rates, increasing the discovery rate of rare OTUs
Short reads, or reads truncated by early low-quality base calls	-	lower	increase	Retain lower-quality but taxonomic usefult reads
Maximize read count for machine-learning tools, cross-metadata OTU counts comparison, etc	-	lower	-	Increased sample size