Master Thesis (Masterarbeit)

Submitted in Partial Fulfillment of the Degree Requirements Master of Science (M.Sc.) in Biotechnology

at the Department of Biotechnology, University of Applied Sciences Mannheim (Hochschule Mannheim), Germany.

by Quynh Nhu Nguyen

Under the Guidance of Dr. Phuc Loi Luu of “on-site Supervisor”, Grant & Innovation Center (GIC), University of Medicine & Pharmacy Ho Chi Minh City (UMP), Vietnam

and Prof. Dr. Markus Gumbel, Hochschule Mannheim, Germany

Mannheim, February 2024

This repository contains scripts used to reproduce our work.

The scripts are designed to be run in the order listed below:

• SRA Sequences Download and Validation
• Preparation GRCh38 reference genome
• Analysis nf-core/sarek pipeline to detect germline variants with the GRCh38 linear reference genome
• Preprocess VCFs and create consensus sequences
• Building pan-exome using nf-core/pangenome
• Up/Downstream pangenome WDL
• Quantification and statistical analysis

Concise explanations of each command's purpose are embedded in comments throughout the script.

Figure 1: NGS data analysis workflow for constructing and analyzing pan-exome. Source: Luu PL, Do HD, 2023; Baaijens et al., 2022.