MetaPhlAn2 - An enhanced metagenomic taxonomic profiling tool
MetaPhlAn2 is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. MetaPhlAn2 is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
MetaPhlAn2 relies on ~1M unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:
- unambiguous taxonomic assignments;
- accurate estimation of organismal relative abundance;
- species-level resolution for bacteria, archaea, eukaryotes and viruses;
- strain identification and tracking
- orders of magnitude speedups compared to existing methods.
Software repository and supporting material
The MetaPhlAn2 tutorial:
The marker information file.
The marker sequences of the MetaPhlAn2 database in fasta format.
How to obtain.
The HMP profiles.
(email-based group and discussion forum):
If you find this tool useful in your research, please cite our paper:
Duy Tin Truong, Eric Franzosa,
Timothy L Tickle, Matthias Scholz, George Weingart,
Edoardo Pasolli, Adrian Tett,
Curtis Huttenhower, and Nicola Segata
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
Nature Methods 12, 902–903 (2015)