Bioinformatics Snakemake Pipeline

Overview

This Snakemake pipeline automates microbial genomic analyses, integrating tools for resistance gene detection, virulence factor identification, typing, and lineage determination.

Installation

1. Clone the repository:

   git clone <repository-url>
   cd <repository-directory>

2. Install dependencies: ```bash conda env create -f environment.yaml conda activate

Running the Pipeline

1. Prepare the samplesheet.tsv:

• Include sample IDs, file paths for reads, and assembly files. Customize config.yaml:

2. Define tools, databases, and analyses for your samples.

3. Execute Snakemake: bash cd workflow snakemake --configfile ../config/config.yaml --cores <N cores>

4. Results:

• Output files will be stored in the directory specified by out_folder

Output Structure

Results are organized by species and sample:

results/
├── Species_1/
│   ├── sample1/
│   │   ├── analysis_1/
│   │   ├── analysis_2/
│   │   └── analysis_3/
│   └── sample2/
|       ├── analysis_1/
|       ├── analysis_2/
|       ...
├── Species_1/
│   ├── sample1/
|       ├── analysis_1/
|       ...
│   
└── logs/