This repo contains the Python libraries for the Precision Immunology Pipeline developed at UCSC.

src/protect/pipeline/ProTECT.py             - The python script for running the pipeline.
src/protect/pipeline/input_parameters.yaml  - The config file for the run that contains all the
                                              necessary parameters for the run.
Flowchart.txt                               - A (super cool) flowchart describing the flow of
                                              the pipeline.

ProTECT uses sequencing information from a patient to predict the neo-epitopes produced in their tumors that can be used in T-cell based, or peptide vaccine based therapies.

All docker images used in this pipeline are available at

                    https://hub.docker.com/u/aarjunrao/

To learn how the pipeline can be run on a sample, head over to the ProTECT Manual

ProTECT is currently in its infancy and is under continuous development. We would appreciate users sharing the level 3 data produced by ProTECT with us such that we can better train our predictive models.