Project: Visual scalability of a pangenome variant analysis design
Description
When a researcher wants to study the genetics of a species, the use of a reference genome is a common approach. A reference genome is the genetic information of one idealized organism of a species. It is assembled by combining DNA from multiple organisms of a species. This method provides a good approximation of the DNA of one individual of a species, but it is limited and biased when someone wants to research the variability of a species.
To research genomic variation a newer approach for studying genetics is more appropriate. This new approach makes use of pangenomes. A pangenome is multiple genomes, created from different strains representing the same species, which can be analyzed in order to understand the species
The goal of this project is to improve a visualization design called PanVA. PanVA is a visual analytics design for variant analysis. While there are already visualization methods and tools created to study and analyze pangenomes, other tools do not provide all the same functions that PanVA does. Most tools either provide only high-level information of pangenomes, are designed for simpler organisms such bacteria, or do not provide metadata together with visualizations. PanVA has been created to handle multiple references in a pangenome together with additional information in the form of metadata, annotations and phylogenetic trees. It is currently focused on the small scale variations in DNA (SNPs), instead of high-level information such as structural variation and PAVs i.e., Presence–Absence Variations.
This project focuses on improving the visual scalability of the current PanVA design such that it can show a larger amount of genetic information while comparing this genetic information against more genomes in one visualization. The design will still focus on the small scale variations instead of high-level information.
Details
- Student
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Kjell Weijts
- Supervisor
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Huub van de Wetering
- Secondary supervisor
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Astrid van den Brandt