Bio Microbiome Functional Prediction

Predicts community functional POTENTIAL from 16S/ITS amplicon ASVs with PICRUSt2 (or q2-picrust2) by phylogenetic interpolation of reference-genome gene content - EPA-ng placement, gappa, castor hidden-state prediction of KO/EC/Pfam copy number, 16S copy-number normalization, and MinPath MetaCyc/KEGG pathways - gated by the NSTI quality index. Covers why predicted function is taxonomy re-encoded (never measured gene content and never activity), the mandatory NSTI report (--max_nsti 2 silently drops novel ASVs), why accuracy IS reference coverage (gut Spearman ~0.8, soil/marine collapse), the circularity trap, and Tax4Fun2/FAPROTAX/BugBase alternatives. Use when inferring …