MetaPhlAn2

The Huttenhower Lab > MetaPhlAn2
MetaPhlAn 2.0

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 on the technical aspects of:

User manual || Tutorial || Forum

 

Citation:
Metagenomic microbial community profiling using unique clade-specific marker genes
Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, Curtis Huttenhower.
Nature Methods, 8, 811–814, 2012

Interested in trying out the latest version? We're in the late-stage testing for a new version MetaPhlAn 3.0

FEATURES

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.
Obtaining MetaPhlAn 2.0

Download MetaPhlAn 2.0 ( metaphlan2.zip ). Review the README or visit the MetaPhlAn 2.0 Github repository for information on installation and how to run.

Synthetic Metagenomes

Synthetic metagenomes can be accessed from here.