Our team is part of the bioinformatics platform at SciLifeLab (NBIS), and a large part of our work involves working with genome assembly in national and international projects. We assemble complete genomic sequences for organisms where this has not been done before, a task that is beyond most research groups, and we support the research community with this expertise. Our projects involve a huge variety of organisms, including fish, fungi, worms, insects, and mammals.
We will be using this compute project to run genome assembly analyses in a EU-funded project called Biodiversity Genomics Europe (BGE), but also potentially for other international or national projects. All of these projects are connected to the Earth Biogenome Project, an umbrella project for many other initiatives, with the aim to sequence the genomes of all species on earth.
BGE is a European project funded through a call in Horizon Europe. It consists of two streams of which we are involved in European Reference Genome Atlas (ERGA). We (through Uppsala University and SciLifeLab) are funded to assemble genomes of European species, most of which are threatened or found in Biodiversity hotspots. Runs until Feb 2026.
The data used will be mostly be long read PacBio Hifi data, and Illumina RNA-seq to be used in annotation. We are mostly working on species from Spain and Slovenia at the moment, of which the stone crayfish Austropotamobius torrentum is influencing our work quite a bit as the genome is huge at 16 Gbp, i.e., more than 5x the size of the human genome, and this greatly increases our need for compute resources and storage.