Version Compatibility

Reference examples tested with: Bracken 2.9+, 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.

Abundance Estimation with Bracken

"Get species-level abundances from my Kraken2 results" → Redistribute reads assigned to higher taxonomic levels down to species using Bracken's Bayesian re-estimation for more accurate abundance profiles.

• CLI: bracken -d db -i kraken2.report -o bracken.output -r 150 -l S

Basic Abundance Estimation