Department: German Human Genome-Phenome Archive
Code number: 2021-0179
The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.
A position as Bioinformatician for the recently launched infrastructure initiative German Human Genome-Phenome Archive (GHGA, www.ghga.de) is available at the DKFZ.GHGA is part of the national program for research data infrastructures (NFDI). As part of the federated European Genome-phenome Archive, GHGA will contribute towards the establishment of an international infrastructure for human genome data. These activities are closely coordinated with leading international initiatives and networks, such as the Global Alliance for Genomics and Health (GA4GH). This infrastructure will support genomics data hubs with software tools for secure data/metadata storage, interactive data portals with data visualization, and streamlined data deposition and acquisition solutions. The GHGA main office, which is coordinated by Prof. Oliver Stegle (Division of Computational Genomics and Systems Genetics), is located at DKFZ in close coordination with the European Molecular Biology Laboratory (EMBL, Dr. Jan Korbel).
We are looking for a bioinformatician or computational biologist to implement and maintain data processing and analysis workflows as part of GHGA. The job will involve implementing a standardized data processing framework that utilizes workflow languages, containerized softwares, and benchmarking. The applications will range from basic data QC and processing to complex variant calling workflows and data integration methods. The successful candidate will be part of an interdisciplinary research and data management team developing and applying a diverse range of state-of-the-art methodology to implement and maintain bioinformatics workflows in a cloud compute environment. The role will involve close cooperation with other partners in the GHGA network, as well as international networks and initiatives.
- Implementing and monitoring a standardized pipeline management framework on cloud environment
- Workflow development and maintenance for NGS data processing and analysis including:
- Somatic and germline variant calling (SNV, Indel, SV, CNV, …)
- Data integration and visualization
- Improvement of bioinformatics workflows with respect to performance and stability
- Testing / benchmarking workflows with cloud deployments
- Development of cloud images for (human) bioinformatics
We offer you the opportunity to help shape one of the most important emerging scientific data infrastructures for the storage and exchange of omics data in Germany.
- Master's degree or equivalent qualification in bioinformatics, computational biology, computer science, statistics, mathematics, or similar background with experience in computational biology / bioinformatics / software development
- > 2 years of experience with software containerization tools like Docker, Singularity
- > 2 years of experience with workflow management tools like CWL, WDL, Snakemake
- Proficiency with UNIX-based systems and relevant programming languages such as Python is a prerequisite
- Previous experience in developing and maintaining complex genomics workflows in a research setting is a prerequisite
- Expertise in software development and cloud computing is beneficial
The ideal applicant should have demonstrated the ability to work independently and creatively. The candidate should have excellent communications skills and be able to articulate clearly the technical needs, set clear goals and work within an interdisciplinary setting, communicating with other partners.
- Interesting, versatile workplace
- International, attractive working environment
- Campus with modern state-of-the-art infrastructure
- Salary according to TV-L including social benefits
- Possibility to work part-time
- Flexible working hours
- Comprehensive further training program
Earliest Possible Start Date: as soon as possible
Duration: The position is initially limited to 2 years with the possibility of prolongation.
The position can in principle be part-time.
Application Deadline: 30.07.2021
Dr. Koray Kirli
Phone +49 (0)6221/42-3466
Please note that we do not accept applications submitted via email.