PDXNet Workflows


The PDXNetwork analysis pipelines for multi-omics data analysis are available as part of the Jackson Laboratory Nextflow pipeline repository. This repository contains multiple analysis pipelines, tools, and scripts that can be easily pulled and utilized by an end user.


Nextflow is a scalable and reproducible scripting language that is used for the development and maintenance of scientific workflows using software containers. Nextflow allows you to write a computational pipeline drawn from a series of intermediate computational steps. The language supports software containers, such as Docker and Singularity, which encapsulate the programs needed to run each step in the workflow. Taken together, the Nextflow pipelines and software containers allow for self-contained, version controlled, immutable, and easily shareable set of workflows.

Reference data to support running all workflows is provided to users external to the Jackson Lab via Globus. Please contact us for access to the Globus collections. Once data have been successfully transferred, the --reference_cache parameter can be used to point workflows at your local reference cache location. Support for additional HPC environments beyond SLURM is also by request.

For questions or comments, please email the Jax NGS Operations group. For issues or bugs found within the workflows themselves, please submit an issue to our GitHub repository.

Supported Workflows

  1. Whole Exome Sequencing with genetic ancestry for patient or PDX

    1. Tumor-only

    2. Tumor-Normal Paired Analysis

  2. RNA Seq for patient or PDX

  3. Whole genome analysis for patient or PDX

    1. Tumor-only

    2. Tumor-Normal Paired Analysis

  4. RNA-Fusion for patient or PDX

Funding is provided by the NIH to the PDXNet Data Commons and Coordination Center (NCI U24-CA224067), and to the PDX Development and Trial Centers (NCI U54-CA224076, NCI U54-CA224083, NCI U54-CA224070, NCI U54-CA283759, NCI U54-CA283766, and U54-CA283762)