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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