https://github.com/clinical-genomics-umea/index_tool
A tool to save sequencing indices in a json-based format.
Science Score: 26.0%
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○Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary
Repository
A tool to save sequencing indices in a json-based format.
Basic Info
- Host: GitHub
- Owner: Clinical-Genomics-Umea
- License: mit
- Language: Python
- Default Branch: main
- Size: 117 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Index Tool
A tool to save sequencing indices in a JSON-based format for Illumina sequencing.
Features
Main reasons for converting to this format are: 1. A need to include override cycle patterns with the indexes. 2. Simplification of making Illumina samplesheet v2 files. 3. Ability to store all data as documents in a MongoDB database.
Indices can be imported for conversion from: - Illumina index kit definition files (TSV) - Custom CSV files
Installation
Create a virtual environment:
bash python -m venv .venv source .venv/bin/activate # On Windows: .venv\Scripts\activateInstall dependencies:
bash pip install -r requirements.txt
Usage
Run the application:
bash
python index_tool.py
Development
Setup Development Environment
Install development dependencies:
bash pip install -r requirements.txtRun tests:
bash pytestCode quality checks:
bash mypy . pylint modules/ black .
License
See the LICENSE file for details.
Owner
- Name: Clinical-Genomics-Umea
- Login: Clinical-Genomics-Umea
- Kind: organization
- Repositories: 1
- Profile: https://github.com/Clinical-Genomics-Umea
GitHub Events
Total
- Push event: 7
Last Year
- Push event: 7