A PluMA pipeline that runs the MiSeq SOP metagenomics example from the Mothur tutorial, followed by some downstream analysis.
Mothur Tutorial is available at: https://www.mothur.org/wiki/MiSeq_SOP Results of their experiment were published in:
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. (2013): Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Applied and Environmental Microbiology. 79(17):5112-20.
To run this pipeline:
- Clone this repository into the pipelines/ directory of PluMA.
- Change to the new Mouse/ subdirectory.
- Run ./getPlugins.sh to automatically download all relevant PluMA plugins.
- Change to the PluMA root directory: 'cd ../../'
- Install the (currently) latest versions of Mothur (1.39.5, mothur.org), Cytoscape (3.6.0, cytoscape.org) and SCons (3.0.1, scons.org) and be sure they are in your system PATH.
- Run 'scons perl=0'
- Run './pluma pipelines/Mouse/config.Mouse.txt'