Background
At the Norwegian Institute of Public health (FHI/NIPH) we perform whole genome sequencing of the SARS-CoV-2 virus as part of the national Covid-19 surveillance. Currently, we are sequencing using different lab techniques and sequencing technologies. For this reason we have many bioinformatics analysis tools and pipelines that are partly overlapping and redundant, sometimes not properly documented and tested, and often inefficient.
The thesis
The aim of this project (or projects) is to develop a unified bioinformatics analysis pipeline that is both flexible (can handle data from different sources), scalable (e.g. can run locally or on a server) and controlled by a workflow manager (e.g. NextFlow). In addition, the pipeline should be openly available (e.g. on GitHub), well documented and tested.
The candidate(s)
We seek highly motivated students with a background from computer science or informatics, but with an interest for biological sciences and bioinformatics. The candidate should be fluent in Bash, and preferably also R or Python. Knowledge about NextFlow or Snakemake is an advantage, but not required. The student will work together with researchers from FHI/NIPH, the Department of Informatics and the Department of Biosciences at UiO.
Contact
If you find this interesting and would like to know more, please contact Jon Bråte (jon.brate@fhi.no). We might also design two or more projects depending on the applicants.