This is the implementation for transmission bottleneck estimation based on beta-binomial sampling.
This code is adapted from: https://github.com/weissmanlab/BB_bottleneck/blob/master/Bottleneck_size_estimation_exact.r For details of how the code works and examples, see the ReadMe of this repo. I vectorised and parallelised the functions, so it runs about 20x faster on 8 cores than the original code.
The input data for this project are a metadata xlsx file with data on each sequence, and NGS diversity data output by VSensus (https://github.com/rjorton/VSensus).
- R 3.6.2+
- rmutil
- parallel
- openxlsx