Chapter 8: Clade-Specific Marker Profiling with MetaPhlAn 4
Chapter 8: Clade-Specific Marker Profiling with MetaPhlAn 4
While Kraken2 indexes entire genome assemblies, MetaPhlAn 4 profiles microbial communities using a curated catalog of ~5.1 million unique clade-specific single-copy marker genes. Because each marker belongs uniquely to a single microbial clade, read depth directly reflects relative cellular abundance without genome size bias.
Advantages of Marker-Gene Profiling
- Extremely low false-positive rate compared to full-genome k-mer classifiers.
- Directly estimates relative cell counts rather than DNA mass proportions.
- Profiles bacteria, archaea, eukaryotic microbes, and viruses simultaneously.
1. Running MetaPhlAn 4
# Profile taxonomic composition using Bowtie2 marker mapping
metaphlan microbial_R1.fastq.gz,microbial_R2.fastq.gz \\
--input_type fastq \\
--bowtie2db /ref/metaphlan4_db/ \\
--nproc 16 \\
-o sample_profile.txt
# Merge profiles across multiple samples into a unified matrix
merge_metaphlan_tables.py sample1_profile.txt sample2_profile.txt > merged_abundance_table.txt