https://github.com/ssi-dk/ssi_analysis_utility
Package for the species specific analysis WP6 MicrobeSeq
https://github.com/ssi-dk/ssi_analysis_utility
Last synced: 7 months ago
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Package for the species specific analysis WP6 MicrobeSeq
- Host: GitHub
- URL: https://github.com/ssi-dk/ssi_analysis_utility
- Owner: ssi-dk
- License: mit
- Created: 2024-11-13T13:25:35.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2025-02-24T13:51:51.000Z (8 months ago)
- Last Synced: 2025-02-24T14:42:47.874Z (8 months ago)
- Language: Python
- Size: 1.07 MB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
``` bash
git clone
cd
```
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 `
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/