Abstract

We will give a summary of the ongoing research in the Goldman group at EMBL -EBI, and of possible projects for the students. First, we will describe our work in large-scale phylogenetics, and in particular the development of a new algorithm for fast and accurate phylogenetic analysis of millions of SARS -CoV-2 genomes. Phylogenetic methods are essential in studying evolution, as exemplified by their use during the SARS -CoV-2 pandemic to identify new variants, reconstruct the origin of the virus, and trace transmission, among many other applications. Phylogenetic analyses have however been hindered by their elevated computational demand and low reliability, issues that we address with a new algorithm specifically developed for scenarios of low divergence between genomes. Secondly, we are working on optimizing the genome-sequencing data gathering capabilities of third-generation technologies. Nanopore sequencing devices now have the ability to ‘reject’ DNA fragments they have started to read, and we have been working on methods that enable good strategies for which fragments to read in their entirety and which to reject. We will describe two experimental contexts in which our methods can be useful, one of which is working and recently published and one of which is still work-in-progress.