Update README.md

README.md

@@ -1,49 +1,67 @@
+# ScanNeo2
+
 -<div align="left">
     <h1>ScanNeo2</h1>
     <img src="https://img.shields.io/badge/snakemake-≥6.4.1-brightgreen.svg">
     <img src="https://github.com/ylab-hi/ScanNeo2/actions/workflows/linting.yml/badge.svg" alt="Workflow status badge">
 </div>
 
-## 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.
+## Introduction
+
+ScanNeo2 is a comprehensive, Snakemake-based workflow designed to predict neoantigens from a variety of sources. It currently supports canonical-splicing, exitron-splicing, gene fusion, indels, and SNVs. This powerful tool provides a streamlined approach to neoantigen prediction, simplifying the process and enabling more efficient research.
 
 ## Getting Started
 
-In principle, Scanneo2 aims to resolve its dependencies automatically and requires only snakemake and snakedeploy.
+### Prerequisites
 
-## Quickstart
+Before installing and using ScanNeo2, make sure you have the following software installed:
 
-Install the [Mamba](https://github.com/conda-forge/miniforge#mambaforge)
+1. [Mamba](https://github.com/conda-forge/miniforge#mambaforge): An open-source package manager. Mamba should be installed independently by the user.
 
-`Snakemake` and `Snakedeploy` will be installed automatically by the following command
+### Installation
 
-```
-mamba env create --file https://raw.githubusercontent.com/ylab-hi/ScanNeo2/main/environment.yml
-mamba activate scanneo2
-```
+To get started with ScanNeo2, follow the steps below:
 
-Deploy Scanneo2
-```
-mkdir -p /path/to/working/directory/
-cd /path/to/working/directory/
-snakedeploy deploy-workflow https://github.com/ylab-hi/scanneo2 . --tag v0.1.0
-```
+1. Create and activate a new environment with Mamba using the environment file from the ScanNeo2 repository:
 
-Configure ScanNeo2 by modifying `config/config.yml`
+    ```bash
+    mamba env create --file https://raw.githubusercontent.com/ylab-hi/ScanNeo2/main/environment.yml
+    mamba activate scanneo2
+    ```
 
-Run the workflow
-```
-cd /path/to/working/directory/
+2. Deploy ScanNeo2:
+
+    ```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.
+
+### Running the Workflow
+
+To run the workflow, use the following command:
+
+```bash
+cd /path/to/your/working/directory/
 snakemake --cores all --use-conda
 ```
-Please consult the [wiki](https://github.com/ylab-hi/ScanNeo2/wiki) for detailed instructions and explanations on the config file.
 
-### Docker
+For more detailed instructions and explanations on how to use ScanNeo2, please consult the [wiki](https://github.com/ylab-hi/ScanNeo2/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.
+
+## Conclusion
 
-We also provide a ready-to-use [Docker Container](https://hub.docker.com/r/yanglabinfo/scanneo2) 
-that can be used to use Scanneo2.
+ScanNeo2 provides an accessible, efficient method for predicting neoantigens. Its comprehensive support for multiple sources of neoantigens, along with its ease of installation and use, make it a powerful tool for researchers in the field. Please don't hesitate to reach out with any questions or feedback - we're always looking to improve ScanNeo2.
 
+## License
 
+ScanNeo2 is licensed under MIT License.
 
+## Contact
 
+If you have any issues or queries about ScanNeo2, please [raise an issue on GitHub](https://github.com/ylab-hi/ScanNeo2/issues/new) or contact us at [[email protected]]([email protected]).