Freyja-Cryptic

Detect cryptic variant circulation in wastewater sequencing data. Beginning with 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

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

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.