Version Compatibility

Reference examples tested with: Kraken2 2.1+, MetaPhlAn 4.1+, pandas 2.2+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Kraken2 Classification

"Classify what organisms are in my metagenomic sample" → Assign taxonomic labels to sequencing reads using exact k-mer matching against a reference database for fast initial classification.

• CLI: kraken2 --db db --paired R1.fastq R2.fastq --report report.txt

Basic Classification