Type: National Project Project
Duration: from 2018 Oct 01 to 2022 Sep 30
Financed by: FCT
Prime Contractor: INESC-ID (Other)
Project Web Site: https://thor.inesc-id.pt/ngphylo/
The current ability to rapidly sequence whole microbial genomes is revolutionizing microbiology and epidemiological surveillance, with high impact on the identification of antimicrobial resistance genes and virulence factors, or on the detection of outbreaks in hospital settings or in the food industry, e.g., by monitoring the spread of antimicrobial resistance, an ever growing concern. It has allowed also more complex phylogenetic analyses based on the whole genome data. The bottleneck has however shifted to data analysis problems. From a computational point of view, a growing concern is how algorithms and tools can be scaled up to analyse thousands of genetic loci in thousands of isolates. This project aims then to: (1) research and design efficient and scalable data structures and algorithms that allow phylogenetic analyses at large scales; (2) develop tools suitable for processing large scale phylogenetic analysis, deployable in cloud and HPC environments; (3) make tools available as reusable components, enabling the construction of more complex parametrizable pipeline workflows; (4) develop and integrate intuitive and user-friendly interfaces.
- INESC-ID (Other)
- Instituto de Medicina Molecular (Other) - Lisboa, Portugal