PluMA: Plugin-Based Microbiome Analysis


  1. Be sure you have Mothur, Cytoscape, and SCons installed and in your system PATH.
  2. If your R is in a non-standard location, set RHOME to its root directory and RSITELIBHOME to its site-library location.
  3. Download PluMA.
  4. Extract the tarball, and change to the resulting pluma/ directory.
  5. Download the P-M16 pipeline.
  6. Extract the tarball from within the pluma/ directory.
  7. Download the MiSeq raw data (Kozich et al. 2013, downloaded May 2016), applicable SILVA database, and RDP training set .
  8. Extract the tarball, again from within the pluma/ directory.
  9. Run 'scons' to compile PluMA.
  10. Run './pluma config.Early.txt' for the Early pipeline, and './pluma config.Late.txt' for the Late pipeline.
Questions? Contact lead developer Trevor Cickovski.




Our lightweight computational backend is implemented in C++ and dynamically loads and sequentially executes user-specified plugins to form a complete pipeline. A plaintext configuration file contains all plugins for the pipeline. Plugins may be written in different languages, including Python, CUDA, C++, R, and Perl. We have also supplied an example pipeline below, which includes two configuration file samples, and instructions on how to compile and run PluMA with the help of SCons (which can be downloaded from Scons) Click below to download the PluMA tar ball or user guide, or to access any other resources.