Repository with simulator code used in paper "Reducing Read Amplification and Re-synthesis in DNA-based Archival Storage".

Reproducing results from the paper

Simulator is written in Python and has minimal dependencies on plotting modules.

1. Install requirements by running pip3 install -r requirements.txt
2. Generate trace by running python3 gen.py 1_80_hint.txt 1/80 which will produce file named 1_80_hint.txt
3. Reproduce Figure 3a-b by running and checking PDFs afterward

python3 sim.py 1_80_hint.txt fig3 1_80_hint.txt fig3
python3 plot3.py

4. Reproduce Figure 4a-b by running and checking PDFs afterward

python3 sim.py 1_80_hint.txt fig4 1_80_hint.txt fig4
python3 plot4.py

6. Reproduce Figure 6 by running and checking PDF afterward

python3 sim.py 1_80_hint.txt fig6 1_80_hint.txt fig6
python3 plot6.py

Each simulation runs 100 times and completes in around 10 minutes.