MetaPhlAn/ MetaPhlAn v2
MetaPhlAn (METAgenomic PHyLogenetic ANalysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data, produced by the Huttenhower lab at Harvard.
MetaPhlAn2 is v2 an update to MetaPhlAn which can identify specific strains and track strains across samples for all species.
Documentation
- MetaPhlAn web home
- MetaPhlAn v2.0 web home
- Citation: if you use MetaPhlAn or MetaPhlAn v2 in your work, please cite:
- Metagenomic microbial community profiling using unique clade-specific marker genes. Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson & Curtis Huttenhower. Nature Methods 9, 811–814 (2012).
- The bioBakery tools and tutorials wiki, which provides software, documentation, and tutorials for methods for microbial community profiling developed by the Huttenhower lab.
Usage
The MetaPhlAn2 dataset is available on Bridges at /pylon5/datasets/community/genomics/metaphlan2.
To see what versions of MetaPhlAn and MetaPhlAn v2 are available type
module avail metaphlan
To see what other modules are needed, what commands are available and how to get additional help type
module help metaphlan
To use MetaPhlAn or MetaPhlAn v2, include a command like these in your batch script or interactive session to load the correct module:
module load metaphlan
module load metaphlan2
Be sure you also load any other modules needed, as listed by the module help metaphlan or module help metaphlan2 command.
