Bioinformatician in genome assembly
Uppsala University, Department of Cell and Molecular Biology
Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.
National Bioinformatics Infrastructure Sweden (NBIS; http://nbis.se), is furthering life science research in Sweden by providing support and developing infrastructure in the field of bioinformatics. The organization is truly national, with 120 bioinformaticians, system developers and data stewards employed at multiple sites in Sweden. NBIS also constitutes the bioinformatics platform at SciLifeLab, a national resource which facilitates research in molecular biosciences by providing access to advanced technologies and technical know-how. With the close connections to data-producing facilities and daily interactions with leading research groups, NBIS is perfectly positioned to enable world class bioinformatics analyses. NBIS is the Swedish node in the European infrastructure ELIXIR for biological information.
NBIS is now looking for a new member to support Swedish and international genome projects on non-model organisms. Part of the work will be done in collaboration with large international reference genome projects such as the European Reference Genome Atlas (ERGA). We can expect a wide range of organisms to work on in these collaborations, including genomes of particular complexity. The person will also be working within our short-term support, where we see a wide variety of different projects coming in from many different fields in biology and medicine. Our bioinformaticians are assigned to these projects depending on areas of expertise. NBIS support needs to continuously change and adapt to the current needs of the Swedish research community, and a willingness and ability to learn is a highly desirable quality for this position.
The position is placed at Uppsala University in the creative environment of the SciLifeLab Uppsala node “The Hub”. Here more than 60 NBIS bioinformaticians, developers, and data stewards are working together, in close proximity of other SciLifeLab facilities and many different research groups. In NBIS you will not be working in isolation, you will be a part of a team. With plenty of colleagues to bounce ideas and share knowledge with, as well as possibilities to participate in internal courses and of course learning from all the exciting support projects, NBIS is a place to grow as a bioinformatician.
The main responsibility is working in genome assembly projects, as a service to Swedish researchers or in international consortia. Work will involve genome assembly using long reads (mostly PacBio HiFi), but also genome annotation, and/or comparative and population genomics. Emphasis will also be on developing improved tools and workflows for internal and external use, for example in the form of Nextflow pipelines. Responsibilities include running analyses, developing bioinformatics tools and workflows, communication with users, staying aware of current developments in the field, writing reports, and teaching.
- At least five years of experience using long-read sequencing data (PacBio or Nanopore) in eukaryotic genome assembly, and expertise in using currently used genome assemblers and assembly QC tools, including a thorough understanding of how to interpret results. Experience of assembly curation is also necessary.
- Experience of working on genome assembly projects of particular complexity regarding for example ploidy, size, or repeat content.
- Experience of developing advanced bioinformatics software and workflows.
- Ability to work efficiently in a Linux command-line environment.
- Excellent communication skills in both written and spoken English are required as is ability to collaborate with scientists of very different backgrounds.
- Emphasis will be placed on personal suitability for the position, such as ability to drive projects and work in a collaborative, yet service-minded environment. A willingness to learn new methods and an ability to acquire new skills is a requirement for this position.
- Knowledge in genome annotation of non-model organisms
- Experience of development of novel long-read assembly software
- Strong ability in R or scripting languages such as Python is considered positive
- Previous experience of working in a support function is also considered beneficial
- Experience of tools used to ensure reproducibility, such as Git, containers, and workflow managers
About the employment
The employment is a permanent position, probationary period may be applied. Scope of employment 100 %. Starting date as soon as possible or as agreed. Placement: Uppsala
For further information about the position, please contact: Manager Dr. Henrik Lantz, email@example.com
Please submit your application by November 29 2022, UFV-PA 2022/4283.