List of participants and affiliations:
- Abhishek Mishra
- Ashwin Babu
- Chrispin Chaguza
- Joshua Levy
- Karthik G
- Lax Iyer
- Tyler Chefin
- Xiaopeng Bian
- Benchmark three existing tools and include a simple SNP threshold as a baseline
- Create simulated dataset and curate real world dataset.
- Run tools on both datasets.
- Compare estimates across tools for both datasets.
- Identify a tool(s) based on estimates and scalability.
- Run selected tool(s) on dataset from a single well sampled location
- Visualize estimates
We selected three well-used tools to be part of our benchmarking analysis: TransPhylo, outbreaker2, and transcluster. We will include a simple SNP threshold to identify transmission clusters as a baseline.
We simulated an outbreak using TransPhylo and simulated sequences from the resulting phylogenetic tree using phastsim. For a real world dataset, we used all the sequences from Massachusetts, USA from the form of July 2010 from GISAID. This time period covers a well characterized superspreading event (Ref).
