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README.md

MetaPhlAn container

Main tool: MetaPhlAn

Code repository: https://github.com/biobakery/MetaPhlAn

Basic information on how to use this tool:

  • executable: metaphlan
  • help: -h
  • version: -v
  • description: MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics.

Additional information:

The MetaPhlAn 4 database has been substantially increased (~21GB) in comparison with the previous 3.1 version. Thus, for running MetaPhlAn 4, a minimum of 25GB or memory is needed. The database can be downloaded from Segatalab FTP or via metaphlan with the following command:

metaphlan --install

Full documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4.1

Example Usage

metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt