Version Compatibility

Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+

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

• 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.

QIIME2 Amplicon Workflow

"Run my amplicon analysis through QIIME2" → Process 16S/ITS amplicon data end-to-end using the QIIME2 CLI with built-in provenance tracking, from import through denoising, taxonomy, and diversity analysis.

• CLI: qiime dada2 denoise-paired, qiime diversity core-metrics-phylogenetic

Import Data