Result of the 2019 Interdisciplinary Bioscience Hackathon (Oxford).
We implemented a simulation of pathogen replication dynamics upon infection based on Leonard et al., Transmission Bottleneck Size Estimation from Viral Sequencing Data, Journal of Virology 91, 14 (2017). We obtain variant sites from deep sequencing for two different viruses (H1N1, H3N2) and, using binomial (binomial_AND_beta_binomial.nb) and beta-binomial (betabinomial.py) sampling methods, try to infer the most likely founder population size N_b in the new host (transmission bottleneck size of viral alleles) as the maximum likelihood value of the simulated distribution.
We check the sanity of our algorithms with computationally generated viral data for a bottleneck size of N_b=50 (generating_simulated_bottlenecks.nb, donorFreq.txt, recipientFreq.txt) and run a population dynamics simulation for three viral populations (ca_all.py).
tidy repository!