Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, MetaPhlAn 4.1+, numpy 1.26+, pandas 2.2+, samtools 1.19+, scipy 1.12+

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.

Strain Tracking

"Track bacterial strains across my samples" → Resolve sub-species variation using genome sketching (Mash/sourmash), average nucleotide identity (fastANI), or within-sample strain profiling (inStrain) for outbreak tracking and transmission analysis.

• CLI: mash dist, sourmash compare, fastANI, inStrain profile

Identify and track bacterial strains at sub-species resolution.

Tool Comparison