Delivering a pangenome approach that drastically improves the analytical power on plant data
To capture and capitalize on genetic variation, the field of comparative genomics is switching from a reference-based approach to pangenomic approaches. The main aim of this project was to improve the scalability of our pangenomics software, called PanTools, for large-scale applications in plant sciences and biotechnology. We envisioned improvements in the data representation, in the construction and annotation algorithms, and in the use of novel technologies like Apache Spark. In addition, we aimed to improve our development efforts and make the code base more sustainable by reorganizing/refactoring, writing proper unit tests, and improving the documentation.
Improving the AARTFAAC processing pipeline
Interpretable large scale deep generative models for Dark Matter searches
Global vegetation water dynamics using radar satellite data
Demonstrating the potential of European Sentinel satellite data
eScience infrastructure for ecological applications of LiDAR point clouds
Arctic impact on weather and climate
Metrics and Access to Global Indices for Climate Projections
The current decline of global biodiversity
Process-based climate simulation: advances in high-resolution modelling and European climate risk...
Processing large datasets on consumer-grade computers
Environmental re-analysis of urban areas: quantifying high-resolution energy and water budgets of...
PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.
General purpose Snakemake pipeline for PanTools v4.
Variant Analysis within Pangenomes.