This repository contains analysis scripts and resources for processing Illumina sequencing data of Hepatitis E virus (HEV) patient samples.

The analysis is conducted using two different reference sequences: one from Sudan and another from Uganda. The respective workflows are implemented as independent pipelines in workflow/Snakefile_sudan and workflow/Snakemake_uganda. Results from each workflow are organized separately in the directories results_sudan and results_uganda.

The configuration file config/config.yaml specifies the reference sequences used and the directories where the input data are located.

Use the files run_pipeline_sudan.sh and run_pipeline_uganda.sh for the execution of the pipelines on Slurm clusters.