Running the ImmunoNX pipeline: predicting neoantigens from raw data to pVACview

The ImmunoNX pipeline is a comprehensive workflow for predicting neoantigens. This video demonstrates all steps of running the pipeline, from setting up your Google Cloud Services account, to launching a pipeline run, to pulling the outputs. We use the HCC1395 cell line as an example dataset for this test run. Find the written instructions located in GitHub here: https://github.com/griffithlab/Immuno... Included in the repository are further details on making your own references, manually reviewing the outputs of an ImmunoNX pipeline run, and how to troubleshoot common problems with a pipeline run. We prefer you use this GitHub repository as a place to reach out and raise questions about running the ImmunoNX pipeline. This preprint manuscript describes our computational pipeline (ImmunoNX) and rigorous manual immunogenomics review criteria for designing neoantigen vaccines: https://arxiv.org/pdf/2512.08226