SUPR
Earth Biogenome Project related assembly projects
Dnr:

NAISS 2024/22-613

Type:

NAISS Small Compute

Principal Investigator:

Henrik Lantz

Affiliation:

Uppsala universitet

Start Date:

2024-05-08

End Date:

2025-06-01

Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Webpage:

Allocation

Abstract

We work for the bioinformatics platform at SciLifeLab (NBIS) and are involved in several genome assembly projects through national and international collaborations. All of these are part of the international Earth Biogenome Project (https://www.earthbiogenome.org), which works as an umbrella project for more narrowly defined projects. One project we are funded in is Biodiversity Genome Europe (BGE; https://biodiversitygenomics.eu), in large part driven by ERGA (https://www.erga-biodiversity.eu). We are currently running most of our analyses at Rackham (UPPMAX), but especially since we we might need to move from that resource once it is no longer available, we would like to start using Dardel and eventually move our project there. The large memory nodes at Dardel are also of big interest to us as some of our projects, especially when we need to work with species with large genomes, require quite a lot of RAM (1 TB or more in some cases). The species we work with are all assigned to us through the projects we are involved in. In BGE most of the species come from Spain or Slovenia, but we also have a few examples of Swedish species. The sequencing is done at SciLifeLab Genomics platform, and my team is responsible to assemble the sequences into as complete genomes as possible and then submit the genomes to European Nucleotide Archive. The genomes will then be picked up by ENSEMBL in the UK for further analysis.