Tonkin-Hill, G., Shao, Y., Zarebski, A.E., Mallawaarachchi, S., Xie, O., Mäklin, T., Thorpe, H.A., Davies, M.R., Bentley, S.D., Lawley T.D., Corander, J. Enhanced metagenomics-enabled transmission inference with TRACS. bioRxiv (2024)
Each distinct analysis is provided in a separate Rmd file. The data needed to reproduce the images is provided in the data subdirectory.
The Bash commands in each Rmd file accurately describe the execution process for running each algorithm. However, they are not configured to run directly from the Rmarkdown document. Instead, these commands were executed separately on a server.