tomermelnik / deepom

DeepOM

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

Installation

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

Getting started

• 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