MetaPhlAn

MetaPhlAn is a bioinformatics tool used for Metagenomic Phylogenetic Analysis. In version 3.x it is possible to perform accurate stain-level microbial profiling.

MetaPhlAn is made available on the UFS HPC via a conda environment which can by loaded as a module.

UFS HPC Usage Example

Follow these steps to use MetaPhlAn:

  1. Start a qwiz or qvnc session. If using a qvnc session, open the Terminal.

  2. Load the MetaPhlAn module (current version is 3.0.14):

    $ module load life-sciences/metaphlan

  3. Initialize the MetaPhlAn environment:

    $ metaphlan_init

  4. MetaPhlAn can now be executed as advertised with one important caveat: You must always specify the bowtie2 database via the --bowtie2db option. The bowtie2 database is stored in a separate location (/dataset/metaphlan/current), however, for convenience, you may simply use $METAPHLAN_DB. For example:

    $ metaphlan input.fasta.gz 
            --input_type fasta 
            --nproc 32 
            --bowtie2db $METAPHLAN_DB
            -o out

Performance Notes

When running MetaPhlAn, use the --nproc flag and set it to the number of cores requested for the job (See the example above in Step 4).

  • 1 Node
  • Memory and number of cores will depend on dataset size

Benchmarks

No benchmarks are available.

UFS HPC Community Guides and Tutorials

  • No community guides are available.

Official site and documentation

Licensing Information

  • MetaPhlAn is free to use and distribute under the terms of the MIT license

Primary citation

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., ... & Segata, N. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife, 10, e65088.

Please remember to cite any additional methods used.

External Guides and Resources