ScanNeo2

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What is ScanNeo2

Scanneo2 is a snakemake workflow for the prediction of neoantigens from multiple sources. In its current state, this includes canonical-splicing, exitron-splicing, gene fusion, indels and snvs.

Getting Started

In principle, Scanneo2 aims to resolve its dependencies automatically and requires only snakemake and snakedeploy.

Prerequisites

Before installing and using ScanNeo2, make sure you have the following software installed:

1. Mamba: An open-source package manager. Mamba should be installed independently by the user.

Installation

To get started with ScanNeo2, follow the steps below:

1. Create and activate a new environment with Mamba using the environment file from the ScanNeo2 repository:

   mamba env create --file https://raw.githubusercontent.com/ylab-hi/ScanNeo2/main/environment.yml
   mamba activate scanneo2
   

   Note: ScanNeo2 requires Snakemake >= 8.x.x is not compatible with Snakemake <= 8.x.x.

2. Deploy ScanNeo2:

mkdir -p /path/to/your/working/directory/
cd /path/to/your/working/directory/
git clone --recurse-submodules https://github.com/ylab-hi/ScanNeo2.git
cd ScanNeo2

3. (Optional) Install HLA-HD

   ScanNeo2 employs HLA-HD for HLA Class II genotyping which is required when ScanNeo2 has been configured to predict class II neoantigens. Due to license reasons it has to be installed manually (download request). Please follow the instructions on the official website. HLA-HD needs to be installed system-wide. In particular, ScanNeo2 calls hlahd.sh. ScanNeo2 has been tested using HLA-HD v1.7.1

<!-- ```bash mkdir -p /path/to/your/working/directory/ cd /path/to/your/working/directory/ snakedeploy deploy-workflow https://github.com/ylab-hi/ScanNeo2 . --tag v0.1.0 ``` -->

3. Configure ScanNeo2 by editing the config/config.yml file. Make sure to adjust parameters to suit your needs and data. Note that the paths in the config file need to be relative to the directory from which you run snakemake.

Running the Workflow

To run the workflow, use the following command:

cd /path/to/your/working/directory/
snakemake --cores all --software-deployment-method conda 

Note that snakemake currently does not support Mamba v2. We recommend to either use Mamba v1, or provide the option --conda-frontend conda.

In addition, custom configfiles can be configured using --configfile <path/to/configfile>. In principle, this merely overwrites the default config, and should include all key/value pairs of the valid config file.

For more detailed instructions and explanations on how to use ScanNeo2, please consult the wiki.

Docker Support

For added convenience, we also provide a ready-to-use Docker Container for ScanNeo2. This container encapsulates the environment required to run ScanNeo2, making it even easier to get started.

Test data

In additon, we provided test data in .tests/integration with configuration and resulting file that can be used to test the installation.

For example, the following will run the the workflow with custom provided variants:

snakemake --cores all --sdm conda --configfile .tests/integration/custom-test/config/config.yaml

Also, the following command will run the workflow with a small raw RNA-seq dataset:

snakemake --cores all --sdm conda --configfile .tests/integration/indel-test/config/config.yaml

System requirements

We recommend to run ScanNeo2 on a system with at least 64GB

Troubleshooting

Please don't hesitate to reach out with any questions or feedback

Citation

@article{Schafer2023Nov,
	author = {Sch{\ifmmode\ddot{a}\else\"{a}\fi}fer, Richard A. and Guo, Qingxiang and Yang, Rendong},
	title = {{ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations}},
	journal = {Bioinformatics},
	volume = {39},
	number = {11},
	pages = {btad659},
	year = {2023},
	month = nov,
	issn = {1367-4811},
	publisher = {Oxford Academic},
	doi = {10.1093/bioinformatics/btad659}
}

License

ScanNeo2 is licensed under MIT License.

Contact

If you have any issues or queries about ScanNeo2, please raise an issue on GitHub.