transmissim is a pipeline that simulates transmission networks, transmission trees, viral genomes evolving along transmission trees, and high throughput sequencing reads. It uses outbreaker, pyvolve, and ART at the moment.
python simulate.py -p params.txt
Different options for simulation parameters can be edited in params.txt.
Transmission network simulation is done using outbreaker.
The transmission tree is currently a binary representation of the transmission network with a python script. We will incorporate coalescent events on the tree in the future.
Sequence simulation along the transmission tree is done using pyvolve.
Read simulation for each sequence, sorted by taxa is done using ART.