PhD position: Genome assembly and pangenome integration

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100%, Zurich, fixed-term

The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates genomic variation within and between livestock populations. The group applies different state of the art technologies to sequence the genomes of farm animals using long and short reads, and applies bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are offering a PhD position on de-novo genome assembly and pangenome integration. 

Project background

Long-read sequencing facilitates the assembly of large mammalian genomes. Sophisticated approaches such as «trio-binning» enable the production of two haplotype-resolved assemblies of reference quality from a sequenced trio. International consortia such as the «Bovine Pan-Genome Consortium» aim at producing haplotype-resolved assemblies for multiple breeds. Pangenomes offer a valuable framework to compare multiple haplotype-resolved assemblies and reveal structural variation within and between breeds. This project builds upon previous projects conducted by the Animal Genomics group that led to variation-aware references , multi-assembly graphs , and most recently, the first bovine pangenome from multiple haplotype-resolved assemblies. Further research is needed to exploit the diversity of an increasing number of haplotype-resolved assemblies, and enable pangenome-wide association testing.

Job description

We are looking for an enthusiastic and highly-motivated candidate to work on bovine genome assembly using long-read sequencing and pangenome integration. The candidate will produce haplotype-resolved assemblies using trio-binning and integrate these newly built assemblies into pangenomes to identify structural differences between breeds. The structural variants will be extrapolated to a large mapping population with phenotypes for dozens of complex traits using comprehensive short-read sequencing data. Association testing will be conducted to detect trait-associated structural variation. A vast amount of short- and log-read sequencing data have already been collected. This is a fixed term position for 4 years with an anticipated start date of March 1st, 2022 (negotiable). The position is based at ETH Zurich, Switzerland. The successful candidate will join the Animal Genomics group  led by Hubert Pausch.

Your profile

You should have a strong research interest in statistical genomics, computational biology, computational genomics, or animal genomics. Experience with a programming language (e.g., python, R) and basic working knowledge with high-performance computing clusters is required. A MSc degree in genetics, genomics, computational biology, bioinformatics, agricultural sciences, animal sciences or disciplines related to the PhD position is required. Affinity to computational genomics, bioinformatics and statistics is a pre-requisite. The writing of scientific papers and active participation in international conferences requires good knowledge of English.

ETH Zurich

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.

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