We have a Bioinformatics PhD position available at The Delft Bioinformatics Lab at TU Delft. Project: Your goal in this project is to create novel algorithms that resolve haplotypes in microbial genomes. Haplotypes refer to the sequence of all individual chromosome copies typically inherited together from a parent. This within-species genetic heterogeneity is one of the missing pieces in many microbial comparative genomics studies aiming to associate genotypes with phenotypes of interest. For many organisms, we poorly understand the contribution of the diversity within an individual, and one of the key reasons is that we don't have the computational tools to study this diversity. With the continued improvements in third generation sequencing technology, combined with the vast quantity of data being deposited publicly, this problem is ready for a solution. You will have three aims: • Implement reference-guided haplotyping from pangenome reference sequence graphs • Explore de novo haplotyping from 3rd generation sequencing data • Investigate copy-number detection at the gene and chromosome scale, and intra-chromosomal DNA variation. Candidate: The ideal candidate has an MSc degree in bioinformatics, computer science, or applied mathematics. Affinity with or experience in biology, genomics and/or sequence analysis are desirable. He/she must be able to work effectively in a multidisciplinary team. The candidate shares our view that communication skills are important, as is the ability to interact with peers, students, and technical staff. Programming and scripting experience is required. Experience in microbial genomics is an advantage. Apply before January 15, 2018 https://www.academictransfer.com/employer/TUD/vacancy/43973/lang/en/ kind regards, Thomas