Project Assistant in bioinformatics, NGI-Uppsala SNP&SEQ

The Department of Medical Sciences (IMV) is a large clinical department with approximately 250 employees and over 900 people affiliated through the Academic Hospital. The department has a broad research profile with strong research groups in various areas. The research takes place in close connection with the clinical activities at the Academic Hospital and includes both basic studies on disease causes and the development and evaluation of improved diagnostics and new treatment methods. More about the department's activities can be found at www.medsci.uu.se.

The SNP&SEQ Technology Platform at IMV is part of the National Genomics Infrastructure (NGI) at SciLifeLab in Uppsala. We offer large-scale services in sequencing (NGS), SNP genotyping, and proteomics to Swedish academia, industry, and international users. The operation consists of a multidisciplinary group of researchers, project coordinators, research engineers, bioinformaticians, system developers, and system administrators. Annually, we analyze more than 60,000 samples and generate more than 400 terabases of data. Data management is mainly carried out on a dedicated cluster designed for handling sensitive data. The cluster (Miarka) is located at UPPMAX, but local servers are also used. More about SNP&SEQ's activities can be read at: https://www.uu.se/forskning/snpseq.

SNP&SEQ always strives to deliver data of the highest quality and we are certified according to the European quality standard ISO/IEC 17025 and accredited by SWEDAC as a testing laboratory.

Do you want to work close to research, supporting a large research field, and working with basic bioinformatics? Do you want to be part of a dynamic and forward-looking team? Then you are welcome to apply for the position as a temporary project assistant.

Duties

• Process sequence data from large-scale sequencing instruments to fastq files.
• Quality control and primary bioinformatics analyses of sequence data in service projects.
• Delivery of data to users.
• Depending on the applicant's skills and experience, the tasks may also include development, improvement, and validation work in existing data processing and analysis systems.

Requirements

• A university degree in bioinformatics, molecular biology, biotechnology, or similar fields, or equivalent qualifications through courses and experience
• Extensive computer skills
• Experience working in a Linux/Unix environment
• Ability to quickly learn new skills
• Excellent verbal and written English skills.

Additional qualifications

• Experience in Python programming
• Experience with shell scripting in a Linux environment
• Experience in data analysis using R packages
• Experience using computer clusters for large-scale calculations or data analysis
• Experience in analyzing data from large-scale sequencing (e.g., whole genome, exome, or RNA-seq) and knowledge about sequencing technologies (Illumina, PacBio, ONT)
• Knowledge of methods and applications in molecular biology and genetics (e.g., PCR, DNA/RNA sequencing, SNP genotyping, etc.)
• Experience with version control using GitHub
• Good verbal and written Swedish skills
• Experience from working in an accredited environment

About the employment
The employment is a temporary position, 12 months. Scope of employment 100 %. Starting date beginning of March or as agreed. Placement: Uppsala

For further information about the position, please contact: Kristina Larsson, head of Data Operations, kristina.larsson@medsci.uu.se, Ulrika Liljedahl, head of unit SNP&SEQ, ulrika.liljedahl@medsci.uu.se

Please submit your application by February 4 2025, UFV-PA 2025/139.

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