A simulation of Hodgkinia transmission in cicadas
Run the script with no arguments to get the usage. The script performs a simulation of cicadas transmitting symbionts to their eggs at random, as used in Campbell, Lukasik et al., presently in review at mBio.
Right now the minimum cells required for each lineage is hard coded (min_cells, line 83). Also all of the coverage values used are hard coded near the beginning (lines ~25-45), but all are commented out except for the ones used at a given time.