metaphlan-profiler

# MetaPhlAn Profiler Skill ## Purpose Enable MetaPhlAn metagenomic profiling for species-level community composition. ## Capabilities - Clade-specific marker gene analysis - Species-level quantification - Strain-level profiling (StrainPhlAn) - Unknown species estimation - Multi-sample heatmaps - Comparative analysis ## Usage Guidelines - Use latest marker database - Profile at species level for most analyses - Apply strain-level analysis when relevant - Visualize community composition - Compare across samples and conditions - Document database versions ## Dependencies - MetaPhlAn4 - StrainPhlAn - mOTUs ## Process Integration - Shotgun Metagenomics Pipeline (shotgun-metagenomics)