DNA Storage Simulator

This monorepository contains code for a research project by Mayank Keoliya and supervised by Djordje Jevdjic, that analyzes and simulates DNA storage.

The structure is as follows:

• CodeReconstruction: Forked from CodeReconstruction, with modifications to aid testing.

  • real_data_clustered.txt: Stores real data in the form:

    [original strand][\n]
    *****************************[\n]
    [copy][\n]
    [copy][\n]
    ...
    [copy][\n]
    [\n]
    [\n]
    [original strand][\n]
    *****************************[\n]
    [copy][\n]
    [copy][\n]
    ...
    [copy][\n]
    ...
    

  • synth_data_clustered.txt: Stores synthetic data in the same form as real_data_clustered, can be generated via the noisy.py module, or DNASimulator
  • compare.sh: Bash script that runs reconstruction algorithms on real_data_clustered and synth_data_clustered

• Scripts: Contains utility scripts

  • get_ground_from_clustered.py: Parses files of the same form as real_data_clustered.txt above, and generates a file strands.txt containing the original strands only. Run using python get_ground_from_clustered.py
  • noisy.py: Naive simulator that takes in a strands.txt file, sequencing coverage, and error probabilities as input and generates noisy copies of multiple clusters in the same form as real_data_clustered.txt