Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, Bracken 2.9+, HUMAnN 3.8+, Kraken2 2.1+, MetaPhlAn 4.1+, fastp 0.23+, matplotlib 3.8+, pandas 2.2+, 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.

Metagenomics Pipeline

"Analyze my metagenomic samples from FASTQ to taxonomic and functional profiles" -> Orchestrate host depletion, Kraken2/Bracken taxonomic classification, MetaPhlAn profiling, HUMAnN3 functional analysis, and AMR gene detection.

Complete workflow from metagenomic FASTQ to taxonomic and functional profiles.

Workflow Overview