bio-metagenomics-metaphlan

name	bio-metagenomics-metaphlan
description	Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
tool_type	cli
primary_tool	metaphlan

MetaPhlAn 4 Profiling

MetaPhlAn 4 uses ~5M clade-specific markers from 26,970 species-level genome bins. Supports both short reads (bowtie2) and long reads (minimap2).

Basic Profiling

# Profile single sample
metaphlan sample.fastq.gz \
    --input_type fastq \
    --output_file profile.txt

Paired-End Reads

# MetaPhlAn processes PE as single file or concatenated
metaphlan reads_R1.fastq.gz,reads_R2.fastq.gz \
    --input_type fastq \
    --output_file profile.txt \
    --mapout sample.map.bz2

Save Mapping Output for Reuse (MetaPhlAn 4.2+)

# First run - save intermediate mapping
metaphlan sample.fastq.gz \
    --input_type fastq \
    --mapout sample.map.bz2 \
    --output_file profile.txt

# Rerun with different settings without realigning
metaphlan sample.map.bz2 \
    --input_type mapout \
    --output_file profile_v2.txt

Long-Read Support (MetaPhlAn 4+)