CRaftID

Software and code associated with CRaftID Paper

Hardware requirements:

Install Instructions:

For targeted_sequencing_analysis and image_processing, refer to the environment YAML file included in this repository. Or create an environment with minimal requirements (Takes a few minutes to install):

conda create -n CRaftID_paper_py3 -c conda-forge \
  python=3.6.8 biopython opencv=3.4.1 ipykernel tqdm
conda activate CRaftID_paper_py3
python -m ipykernel install --user --name CRaftID_paper_py3 --display-name "CRaftID"

For neural network classifier, refer to the neural_net_classifier README.md, or create an environment with minimal requirements:

IF USING GPUs:

conda create -n nn_classifier_gpu -c conda-forge -c anaconda \
  opencv tqdm scikit-learn keras-gpu
conda activate nn_classifier_gpu

IF USING CPU only:

conda create -n nn_classifier -c conda-forge -c anaconda \
  opencv tqdm scikit-learn keras
conda activate nn_classifier_gpu

Usage:

Refer to the notebooks within each section:

• targeted_sequencing_analysis
• image_processing
• neural_net_classifier

Runtime is not more than a few minutes total for the single image dataset provided here.