The Department of Aquatic Sciences and Assessment is working with applied environmental science, with a national responsibility for assessing the condition of Swedish surface waters with respect to water chemistry, pollution and aquatic biota.

The department has about 140 employees. The research focuses on geochemical and hydrological processes, aquatic ecology and biodiversity, as well as on aquatic ecotoxicology and environmental chemistry.

The department is part of a Soil-Water-Environment cluster, a recently established competence centre for landscape-level processes that also includes the Departments of ‘Soil and Environment’ and ‘Energy and Technology’. The breadth of expertise among the 300 members in combination with a well-equipped infrastructure creates a unique platform for high quality research as well as environmental monitoring and assessment.


We are looking for a Research assistant to be placed at the Department of Aquatic Sciences and Assessment, SLU. The candidate will incorporate to a recently established division (Microbial Ecology) and assist with establishing a new research line. The project aims to develop an automated bioinformatics pipeline for analyzing pangenome dynamics from environmental metagenomic datased.

For this, we will extend the pipelines existing in the laboratory by integrating additional tools aimed to perform species-level clustering and pangenome assembly. The candidate will be responsible for pipeline development, validation and documentation. The candidate will also be expected to contribute to preliminary analysis of real datasets.

The Department research laboratories are a dynamic and stimulating workplace with potential for future career development and opportunities to work with other biological methods such as DNA isolation and sequencing, flow cytometry, microscopy, microbial cultivation and experiments.


We are seeking a highly motivated candidate with a Master’s degree in bioinformatics or related subject. Candidates are required to demonstrate good knowledge and previous experience with UNIX/shell, the Nextflow programming language and at least an additional programming language with applications for bioinformatics.

Knowledge and practical experience on metagenomics and pangenomics is required. Further knowledge of aquatic microbiology, molecular biology and microbial ecology/evolution is desirable and will be considered merits.

We are looking for a candidate who can work independently and in a structured manner, with attention to detail and proper documentation of the work performed. Personal qualities such as responsibility, independent problem-solving and interpersonal skills and will be considered as further merits. The ability to communicate well in English is a requirement.

Place of work: Uppsala

Form of employment: Fixed term employment of 6 months with possibility of prolongation.

Extent: 100%

Starting date: 2023-11-01 or according to agreement.

Application: We welcome your application no later than 2023-09-15, please use the button below.

The Swedish University of Agricultural Sciences (SLU) has a key role in the development for sustainable life, based on science and education. Through our focus on the interaction between humans, animals and ecosystems and the responsible use of natural resources, we contribute to sustainable societal development and good living conditions on our planet. Our main campuses are located in Alnarp, Umeå and Uppsala, however, the university also operates at research stations, experimental forests and teaching sites throughout Sweden.

SLU has around 3,000 employees, 5,000 students and doctoral students and a turnover of over SEK 3 billion. We are investing in attractive environments on all of our campuses.

We strive to provide a work environment characterised by inclusivity and gender equality, where different experiences generate conversations between people and pave the way for science, creativity and development. Therefore, we welcome applications from people with diverse backgrounds and perspectives.

Contact person Fernando Puente-Sánchez, Researcher +46-70-1679034

Apply now

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