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Standardize Metaphlan Specifications

Process Details

  • Name: standardize_metaphlan
  • Process UUID: f9315shoquw3hadsbt863nevu7yoe6
  • Process Group: short_read_taxonomy

Overview

This process converts MetaPhlAn output to a standardized format across different taxonomic ranks (species, genus, etc.). It takes raw MetaPhlAn taxonomic profiling results and transforms them into consistent CSV format files for downstream analysis and visualization.

This process is implemented in Bash, which invokes a Python script for data standardization and formatting.

Key Functionality

  • Format Standardization: Converts MetaPhlAn output into consistent CSV format across taxonomic levels
  • Taxonomic Rank Processing: Processes data at multiple taxonomic ranks (species, genus, family, etc.)
  • Abundance Filtering: Applies minimum relative abundance thresholds to filter low-abundance taxa

Input/Output Specification

Inputs

Required Inputs

  • MetaPhlAn Output
    • Description: Raw taxonomic profiling results from MetaPhlAn analysis
    • Format: MetaPhlAn format file

Outputs

  • Standardized CSV Files
    • Description: Multiple CSV files containing standardized taxonomic abundance data at different taxonomic ranks
    • Format: CSV format (6 output files generated)

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Minimum Relative Abundance
    • Description: Minimum relative abundance threshold for filtering taxa
    • Default value: Set via params.min_rel_abund

References & Resources

  • Tool Documentation: Contact the team for details on standardize_metaphlan.py