transmissim simulates genomic reads from epidemiological transmission networks
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README.md

Build Status codecov

Overview

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.

Usage

To run:

python simulate.py -p params.txt

Different options for simulation parameters can be edited in params.txt.

Pipeline Organization

Transmission Network

Transmission network simulation is done using outbreaker.

Transmission Tree

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

Sequence simulation along the transmission tree is done using pyvolve.

Read Simulation

Read simulation for each sequence, sorted by taxa is done using ART.