Sript requires the following dependencies:
- python 2.7.12
- networkx 2.1
- pyemd 0.5.1
- numpy 1.15.1
- biopython 1.72
- DeNovoAssembly
All python modules, except DeNovoAssembly can be installed through pip. DeNovoAssembly can be downloaded from https://github.com/guojingyu/DeNovoAssembly For convenience, de_bruijn_graph.py, eulerian.py and utils.py scripts of DeNovoAssembly library can be copied into kemd directory.
Once installed, algorithm can be executed using the following command:
python find_all_pairwise_EMD_without_explicit_global_graph_simulated_miseq_reads_clean.py ./test_data ./test_output
Example of test input can be found in test_data directory.