https://github.com/andersen-lab/freyja-cryptic

https://github.com/andersen-lab/freyja-cryptic

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/andersen-lab/freyja-cryptic
• Owner: andersen-lab
• Created: 2024-11-12T14:38:16.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-01-28T16:21:17.000Z (over 1 year ago)
• Last Synced: 2025-04-12T06:59:20.883Z (about 1 year ago)
• Language: Python
• Size: 664 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# Freyja-Cryptic

Detect cryptic variant circulation in wastewater sequencing data. Beginning with ![Freyja covariants](https://andersen-lab.github.io/Freyja/src/usage/covariants.html) outputs, this tool will query each mutation cluster occurring on the same read pair to determine if the cluster has been previously detected in clinical sequencing.

## Installation

```bash

git clone https://github.com/andersen-lab/freyja-cryptic.git && cd freyja-cryptic

mamba create -n freyja-cryptic

mamba env update -n freyja-crypic -f environment.yml

mamba activate freyja-cryptic

```

## Usage

```bash

python detect-cryptic.py --covariants_dir /path/to/covariants --output_dir /path/to/output --metadata /path/to/metadata.csv --max_clinical_count (default=10)

```

Upon running the script for the first time, a prompt will appear asking to authenticate with GISAID. This is needed to access the clinical data.