FEET pipeline summary

FEET is an adaptable workflow that allows one to identify and tally putative EET proteins from sample(s) of genomes or metagenome assembled genomes (MAGs). In this case, a sample is simply a folder of genomes, and the output files will be grouped/titled according to each sample name. FEET uses FeGenie and will incorporate additions to FeGenie if a more recent version is downloaded rather than the one shown here. FEET combines FeGenie results with python scripts that search for beta-barrel outer membrane porins and outer surface multiheme cytohromes, using a cellular localization prediction resource (Cello V2).

How do I use my FEET?

Step 1: look at example outputs to see if this is what you want: FEET-example-outputs/

Step 2: get set up by following the instruction in the README's inside FEET-setup/

Step 3: follow steps described in FEET-pipeline-scripts/PipelineScript.txt

What if FEET misteps?

If there are any bugs or questions. Feel free to contact my email with "FEET_Pipeline" in the subject line: cnolmsted@wisc.edu

There are certainly ways to improve this pipeline, such as automating the Cello step somehow, and therefore being able to automate the whole thing. If you succeed in doing this, please consider sharing so I can add it to the pipeline!