MetaPhlAn 3
MetaPhlAn 3 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. StrainPhlAn 3 is 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.
MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v30_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) identified from ~100,000 reference genomes (~99,500 bacterial and archaeal and ~500 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 and memory usage compared to existing methods
- metagenomic strain-level population genomics
Software repository and supporting material
Software repository
of MetaPhlAn2:
https://github.com/biobakery/metaphlan/tree/3.0
The MetaPhlAn2 tutorial:
https://github.com/biobakery/biobakery/wiki/metaphlan3
The marker information file.
Download.
User support
(email-based group and discussion forum):
https://forum.biobakery.org/c/Microbial-community-profiling/MetaPhlAn2
For comments and
question please write to our
user support group
or contact directly the Segata
lab.
Citation
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)