TABLE 2.

Configuration of MSE 2 for each sequence type and recommended software for preprocessing

Search type	Applicable sequence type	Recommended software(s) for sequence preprocessing (reference)	Similarity metrics
By OTU	16S rRNA gene amplicon	Parallel-META 3 (29), QIIME (35)	Meta-Storms (33)
By species	Shotgun WGS	MetaPhlAn 2 (25)	Dynamic Meta-Storms (34)
By function	16S rRNA gene amplicon and shotgun WGS	Parallel-META 3 for a 16S rRNA gene amplicon, integrated with a C++ implantation of PICRUSt 2 (32); HUMAnN 2 for shotgun WGS (26)	Bray-Curtis