Detection of cryptic mutation profiles in SARS-CoV-2 metagenomes through variant co-occurrence

1. Install Nextflow (if not yet in working environment) via

conda create -n nextflow -c bioconda nextflow==25.10.2
conda activate nextflow

2. Download pipeline

git clone https://github.com/Krannich479/crymco.git
cd crymco

3. Fill I/O section (files) in nextflow.config
4. Run pipeline via

nextflow run main.nf -profile local,mamba

• Alignment + Variant Calling + Phasing + Haplotagging
• • devider
• Reformatting haplotype table into Nextstrain variant nomenclature
• • bin/devider2hdm.py
• Normalize mutation frequency table + join with haplotype table + compute distance matrix + compute single-linkage hierarchical clustering
• • bin/haploDistance.py

• The current PNG of the last pipeline step is hardly readable as static image. Needs adjustment; likely in python script
• Numeric output would be usefull I guess. Printing/using the distance matrix is likely a good starting point
• There might be a more sophisticated clustering method for this task than currently implemented (e.g. skbio has a module for UPGMA)
• Generating the mutation frequency table needs documentation for third-party users