Advisor: Dirk Steinke, Integrative Biology
Metabarcoding is a becoming a popular tool for monitoring and assessing biodiversity. A gene region is amplified from bulk samples and sequenced using high throughput sequencing technology.
DNA Sequences are clustered into operational taxonomic units (OTUs) which are outputted into tables that are difficult to visualize especially for large complex datasets. This project would focus on creating tools to visualize OTU tables comprised of many different sampling sites and varying OTU read counts. Additionally, this project would improve visualization of BLAST hit tables (or comparable methods for taxonomic assignment) for OTUs to identify problematic sequences and conflict in taxonomic assignment.
Prospective students would develop a R package that:
- Builds on various OTU clustering strategies
- Provides alternative visualization options for OUT tables with varying sbstructure