MetaPhlAn 3


MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:

  • up to 25,000 reads-per-second (on one CPU) analysis speed (orders of magnitude faster compared to existing methods);

  • unambiguous taxonomic assignments as the MetaPhlAn markers are clade-specific;

  • accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction of reads);

  • species-level resolution for bacteria, archaea, eukaryotes and viruses;

  • extensive validation of the profiling accuracy on several synthetic datasets and on thousands of real metagenomes.

For more information, please check its user guide at:


  • 3.0.14

  • 3.0.9




The lastest version of database(mpa_v30) has been downloaded and built in /depot/itap/datasets/metaphlan/.


You can load the modules by:

module load biocontainers
module load metaphlan/3.0.14

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run MetaPhlAn on our cluster:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH --job-name=MetaPhlAn
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers metaphlan/3.0.14

metaphlan SRR11234553_1.fastq,SRR11234553_2.fastq --input_type fastq --nproc 24 -o profiled_metagenome.txt --bowtie2db $DATABASE  --bowtie2out metagenome.bowtie2.bz2