Version Compatibility

Reference examples tested with: DADA2 1.30+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Taxonomy Assignment

"Assign taxonomy to my ASVs" → Classify amplicon sequence variants against reference databases (SILVA, GTDB, UNITE) using naive Bayes or exact-matching approaches for taxonomic annotation.

• R: dada2::assignTaxonomy() with SILVA/GTDB reference
• CLI: qiime feature-classifier classify-sklearn for QIIME2 workflows

DADA2 Naive Bayes Classifier