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Metaphlan Specifications

Process Details

  • Name: metaphlan
  • Process UUID: f931gl21j64osusy62a6bhl8rg9qz8
  • Process Group: short_read_taxonomy

Overview

This process classifies microbial community composition using marker genes through MetaPhlAn (Metagenomic Phylogenetic Analysis). It performs taxonomic profiling of metagenomic shotgun sequencing data by identifying clade-specific marker genes and estimating the relative abundance of different microbial taxa in the sample.

This process is implemented in Bash, which invokes the MetaPhlAn tool for taxonomic classification and abundance estimation.

Key Functionality

  • Taxonomic Classification: Identifies and classifies microbial taxa present in metagenomic samples using clade-specific marker genes
  • Relative Abundance Estimation: Calculates the relative abundance of detected taxa with read statistics
  • Multi-format Output Generation: Produces results in multiple formats including BIOM, SAM, and text formats for downstream analysis
  • Bowtie2 Alignment: Performs sequence alignment against the MetaPhlAn database using Bowtie2 for accurate taxonomic assignment

Input/Output Specification

Inputs

Required Inputs

  • MetaPhlAn Database

    • Description: Pre-built MetaPhlAn reference database containing clade-specific marker genes
    • Format: metaphlan database format

  • Sequencing Reads

    • Description: Raw metagenomic sequencing reads to be taxonomically classified
    • Format: FASTQ

Outputs

  • SAM Files

    • Description: Sequence alignment files showing read mappings to marker genes
    • Format: SAM

  • MetaPhlAn Output Files

    • Description: Primary taxonomic profiling results with relative abundances and read statistics
    • Format: metaphlan format

  • Text Report Files

    • Description: Processed taxonomic abundance tables in tab-delimited format for easy analysis
    • Format: TXT

  • BIOM Files

    • Description: Biological Observation Matrix files containing taxonomic abundance data in standardized format
    • Format: BIOM

References & Resources

  • Tool Documentation: Contact the team for details on MetaPhlAn configuration and usage
  • Related Papers: Blanco-Míguez, A., Beghini, F., Cumbo, F. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 41, 1633–1644 (2023). https://doi.org/10.1038/s41587-023-01688-w