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README.md

locimend

locimend is a tool that corrects DNA sequencing errors using Deep Learning.

Technologies

  • Tensorflow
  • Biopython

Installation

This project uses Nix to ensure reproducible builds.

  1. Install Nix (compatible with MacOS, Linux and WSL):
curl -L https://nixos.org/nix/install | sh
  1. Clone the repository:
git clone https://git.coolneng.duckdns.org/coolneng/locimend
  1. Change the working directory to the project:
cd locimend
  1. Enter the nix-shell:
nix-shell
  1. Install the dependencies via poetry:
poetry install

After running these commands, you will find yourself in a shell that contains all the needed dependencies.

Usage

The following command creates the dataset, trains the Deep Learning model and shows the accuracy:

poetry run python src/model.py