Biomedical Data Analysis Platform

Home > Analysis Platform > Taxonomic profiles

Introduction：

MetaPhlAn 4 is a computational tool for high-resolution taxonomic profiling of metagenomic shotgun sequencing data. It uses a database of ~5.1 million unique clade-specific marker genes to identify and quantify microbial taxa (from phylum to strain level) with high specificity and low false-positive rates. Compared to alignment-based methods, MetaPhlAn 4 is faster, more memory-efficient, and robust against host contamination. Version 4 introduces improved strain-level tracking, integration with HUMAnN 3 for functional profiling, and an expanded marker database covering bacteria, archaea, viruses, and eukaryotes.

Workflow Case Analysis Versions Manual Download

Marker Mapping: Aligns quality-controlled reads against the MetaPhlAn marker database using Bowtie2.
Taxon Identification: Identifies present taxa based on unique marker coverage; filters spurious hits using statistical thresholds.
Abundance Estimation: Normalizes marker coverage by genome length and total mapped reads to compute relative abundances.
Strain-Level Profiling (Optional): Detects strain-specific markers and SNPs for tracked strains when --strainprof is enabled.
Output: Generates a tab-separated profile table, optional BIOM format, and log files.

Data

Results

Usage