SnakeBITE

A user-friendly Shiny GUI developed in python for customize and launch modular genomics data analysis pipelines using Snakemake, from Nanopore Oxford Technologies data.

Installation

0. Prerequisites

• Conda is required to be installed on your system for basic program use.
• Git is required to be installed on your system for cloning the repository.
• Dorado (Due to licensing restrictions, please download and install Dorado separately)

1a. Clone the repository

To download this software, you can clone this repository on your local system, inside your current directory (from now on called /path/to/SnakeBITE) by executing the following commands:

git clone https://github.com/Lab-CoMBINE/SnakeBITE.git
cd path/to/SnakeBITE

2. Main conda environment Installation

From /path/to/SnakeBITE, please make sure to create and activate the main conda environment:

conda env create -f environment.yaml
conda activate snkbt_snakemake_env

3. Individual tools conda environment installation

From /path/to/SnakeBITE, please set up each conda environment with the featured data analysis tools that you do not already have:

Create deepvariant conda environment

conda env create -f envs/snkbt_deepvariantenv.yaml

Create longshot conda environment

conda env create -f envs/snkbt_longshotenv.yaml

Create Nanocaller and Clair3 conda environment

conda env create -f envs/snkbt_nanoclair3env.yaml

Create sniffles conda environment

conda env create -f envs/snkbt_sniffles2env.yaml

Create svim and cutesv conda environment

conda env create -f envs/snkbt_svimcutesvenv.yaml

Create vep conda environment

conda env create -f envs/snkbt_vepenv.yaml

4. Specific dependencies Installation

Make sure to install extra requirements from the provided file:

pip install -r requirements.txt

Usage

Shiny GUI Launch

Launch SnakeBITE GUI using the following command line:

shiny run --reload path/to/SnakeBITE/app/app.py

Congratulations: you are inside SnakeBITE now. Follow the instructions in the web browser page to build and launch your own modular pipeline on ONT data.

Project Structure

Brief schematic of the project:

SnakeBITE/
├── app/
│   ├── app.py                          # Main shiny application
│   ├── server_launch.py                # Pipeline launcher script
│   ├── server_utils.py                 # Utility functions for the Shiny server side
│   ├── ui_pipelines.py                 # Script for pipeline definition on Shiny ui side
│   ├── ui_toolparameters.py            # Script for parameter configuration on Shiny ui side
│   ├── ui_utils.py                     # Utility functions for the Shiny ui side
│   ├── filexplorer_ssh.py              # Script for appearance and explore ssh and sftp server
│   ├── compiler.py                     # Snakemake command compiler script
├── config.yaml                         # Main Snakemake config.yaml file
├── environment.yaml                    # Main conda environment
├── requirements.txt                    # Extra pip dependencies
├── workflow/   
    ├── envs/   
        ├── snkbt_deepvariantenv.yaml   # conda env for deepvariant tool
    │   ├── snkbt_longshotenv.yaml      # conda env for longshot tool
    │   ├── snkbt_nanoclair3env.yaml    # conda env for Nanocaller and Clair3 tools
    │   ├── snkbt_sniffles2env.yaml     # conda env for sniffles tool
    │   ├── snkbt_svimcutesvenv.yaml    # conda env for svim and cutesv tools
    │   ├── snkbt_vepenv.yaml           # conda env for vep tool
    ├── scripts.py                      # Snakemake python helper functions
    ├── Snakefile                       # Snakemake workflow definition

Contribution

If you want to contribute to this repository, please follow these steps:

1. Fork this repository
2. Create a branch -> git checkout -b feature/ProposedFeature
3. Commit your modifications -> git commit -m 'Add some ProposedFeature'
4. Push your branch -> git push origin feature/ProposedFeature
5. Open a pull request

License

This project is licensed under the GNU General Public License v3.0 (GNU GPLv3). See the LICENSE file for details.

Included Tools and Their Licenses

• Snakemake - MIT License
• Shiny for Python - MIT License
• Dorado - Public License Version 1.0 (requires separate download)
• minimap2 - MIT License
• samtools - MIT/Expat License
• SVIM - GNU GPL v3
• Sniffles2 - MIT License
• cuteSV - MIT License
• Gasoline - MIT License
• Longshot - MIT License
• NanoCaller - MIT License
• Clair3 - Copyright 2021 The University of Hong Kong
• DeepVariant - MIT License
• annotSV - GNU GPL v3
• VEP - Apache v2 License