Version Compatibility

Reference examples tested with: HUMAnN 3.8+, MetaPhlAn 4.1+, matplotlib 3.8+, pandas 2.2+, scanpy 1.10+, scipy 1.12+, seaborn 0.13+

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.

Functional Profiling

"What metabolic pathways are present in my metagenome?" → Profile functional potential of metagenomic samples to obtain pathway abundances and gene family counts using translated search against UniRef and MetaCyc.

• CLI: humann --input reads.fastq --output results/ (HUMAnN3)

Profile the functional potential of metagenomic samples using HUMAnN3 to get pathway and gene family abundances.

HUMAnN3 Workflow