Background
The Norwegian Institute of Public Health (FHI/NIPH) performs genome sequencing of hepatitis B virus (HBV) as part of the national molecular surveillance. HBV is a major global health challenge, causing chronic infections that can lead to severe liver disease, including cirrhosis and liver cancer. Despite effective vaccines and antiviral treatments, HBV continues to circulate and evolve, partly due to the emergence of resistant variants. Identifying resistance mutations is therefore crucial for disease control, treatment management, and long-term monitoring.
To achieve this, bioinformatics tools are needed that can process viral gene and genome sequences and detect known resistance-associated mutations in a reproducible way.
The thesis
The goal of this project is to develop an open-source, stand-alone software for identifying resistance mutations in HBV genomes. The tool should be:
- lightweight and easy to install (e.g. via conda or pip),
- compatible with standard bioinformatics workflows and file formats (FASTA and BAM),
- well documented and openly available on GitHub.
The student will design and implement the tool—preferably using Python or another widely used programming language—and test it using real HBV sequence data from FHI. The resulting software will support ongoing HBV surveillance and resistance monitoring in Norway and contribute to the global understanding of HBV evolution.
The candidate
We seek a motivated student with a background in informatics, computer science, or bioinformatics. The candidate should be comfortable with Bash and common programming languages (e.g., Python) and familiar with version control systems such as Git/GitHub. Experience with workflow management (e.g. Nextflow, Snakemake) or biological data analysis is an advantage but not required. The student will collaborate with researchers at the Norwegian Institute of Public Health and the University of Oslo.
Contact
For more information, please contact Jon Bråte (jon.brate@fhi.no) or Torbjørn Rognes (IFI). The project can be adapted in scope and complexity depending on the interests and background of the student.