Bioinformatician with focus on systems development, NGI Uppsala, SNP&SEQ

SciLifeLab; Uppsala kommun; On-site; SEK 495 000 - 716 000; Full time

Job summary

A leading research institution in Uppsala is seeking a technology-driven bioinformatician to join their Data Operations group. The successful candidate will design and maintain systems for analyzing large-scale genomics data while collaborating with multiple units. This is a permanent position requiring a university degree in bioinformatics and at least three years of experience in system development. Excellent skills in Python and Unix/Linux are essential.

Benefits

Dynamic and collaborative work environment

Access to cutting-edge research

Qualifications

• At least three years of experience in bioinformatics-related system development.
• Excellent verbal and written English skills.
• Ability to quickly learn new skills.

Responsibilities

• Designing and maintaining systems for analyzing large-scale genomics data.
• Managing data on a high-security cluster.
• Automating data handling and system integrations.

Skills

Python

Unix/Linux

Git

Data processing pipelines

Agile methodologies/Scrum

Education

University degree in bioinformatics or related field

Tools

Nextflow

Docker

Job description

Overview

Uppsala University, 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 SciLifeLab National Genomics Infrastructure (NGI) in Uppsala. We provide large-scale sequencing (NGS), SNP genotyping, and proteomics services to Swedish academia, industry, and international users.

Read more

Our multidisciplinary team includes researchers, project coordinators, research engineers, bioinformaticians, system developers, and system administrators. Each year, we process more than 60,000 samples and generate over 400 Terabases of data. More about our activities and services can be found at: https://www.uu.se/forskning/snpseq and https://ngisweden.scilifelab.se/

We are proud to deliver high-quality data and are accredited by SWEDAC as a testing laboratory under the ISO/IEC 17025 quality standard.

We are now looking for a technology-driven bioinformatician to join our Data Operations group. The group at the interface of bioinformatics and IT, ensuring smooth and efficient data handling across the unit.

Duties

Your Responsibilities Will Include, But Not Me Limited To

• Designing, developing, and maintaining open-source systems for processing and analyzing large-scale genomics data.
• Managing data on our dedicated high-security cluster Miarka at UPPMAX, as well as on local servers.
• Automating data handling and integrating systems for laboratory tracking (samples, steps, reagents), document management, and KPI visualization.
• Developing and supporting internal systems, including LIMS integrations and existing DevOps solutions (e.g., Ansible, GitLab).
• Establishing, maintaining, and validating system documentation.
• Collaborating closely with Uppsala University IT, UPPMAX, and other SciLifeLab units (such as NBIS).

Examples of systems and tools you will work with include Arteria, CheckQC, nf-core pipelines, and Nextflow. These tools support large-scale genomics workflows and data processing.

Are you interested in working close to cutting-edge research and supporting a broad scientific community? Do you thrive in a dynamic and collaborative environment where you can both use and develop your technical skills? Then this position may be the perfect fit for you.

Requirements

• University degree in bioinformatics, computer science, IT, or a related field.
• At least three years of documented professional experience in bioinformatics-related system development.
• Excellent knowledge of Python or similar programming languages.
• Experience using Git for version control.
• Ability to quickly learn new skills.
• High proficiency in Unix/Linux environments.
• Excellent verbal and written English skills.

Additional Qualifications

In addition to the qualification requirements listed above, we also value previous experience in one or more of the following areas:

• Doctoral degree including bioinformatics with a focus on genomics, genetics, or similar area
• Experience in developing data processing pipelines, such as Nextflow or similar systems.
• Computer clusters and distributed systems.
• Virtual environments, e.g., Docker or Apptainer.
• Methods for software deployment (e.g. Ansible) and continuous integration.
• Familiarity with methods and applications in molecular biology and genetics
• Understanding of information security.
• Agile methodologies/Scrum.
• ELK stack or similar log management systems.
• Experience in LIMS development.
• Experience in data management with public databases for FAIR data handling, such as ENA or ArrayExpress.
• Experience working in quality-assured environments, e.g. according to ISO 17025 or ISO 27001.
• Good verbal and written Swedish skills.

About The Employment

The employment is a permanent position (6 months probationary period may be applied). Scope of employment 100 %. Starting date as agreed. Placement: Uppsala

For further information about the position, please contact: Kristina Larsson, head of Data Operations, [e-mail], Ulrika Liljedahl, head of unit SNP&SEQ, [e-mail]

Please submit your application by 29th of September 2025, UFV-PA 2025/2703.

Are you considering moving to Sweden to work at Uppsala University? Find out more about what it´s like to work and live in Sweden.

Uppsala University is a broad research university with a strong international position. The ultimate goal is to conduct education and research of the highest quality and relevance to make a difference in society. Our most important asset is all of our 7,600 employees and 53,000 students who, with curiosity and commitment, make Uppsala University one of Sweden’s most exciting workplaces.

Read more about our benefits and what it is like to work at Uppsala University

https://uu.se/om-uu/jobba-hos-oss/

The position may be subject to security vetting. If security vetting is conducted, the applicant must pass the vetting process to be eligible for employment.

Please do not send offers of recruitment or advertising services.

Submit your application through Uppsala University’s recruitment system.