DeepOM

DeepOM is a Python deep-learning software for optical mapping of DNA images to a genome reference. See the paper for details.

For inference only: Running the example script

Ensure you use python >= 3.10

cd tool
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt
python example.py

conda env create -f environment.yml
conda activate deepom
pip install -r requirements.txt
pip install -e .

Reproducing the figures from the paper: See Jupyter notebooks in the figures dir.

Running the localizer net training:

conda activate deepom
python deepom/localizer.py

Running the benchmark:

conda activate deepom
python deepom/bionano_compare.py