coolneng
/
locimend
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity
49 Commits 1 Branch 2 Tags 3 MiB
PureBasic 94.3%
Python 3.3%
Nix 2.4%
Go to file
coolneng e07d0dcdbf
Change Flatten layer, loss function and add Input 		2021-06-26 17:52:20 +02:00
data Add datasets 2021-06-10 13:18:25 +02:00
docs Add the Jupyter notebook 2021-06-15 01:00:45 +02:00
logs Create logs directory 2021-06-15 00:38:09 +02:00
nix Change nixpkgs channel to unstable 2021-05-05 23:53:48 +02:00
src Change Flatten layer, loss function and add Input 2021-06-26 17:52:20 +02:00
.gitignore Create logs directory 2021-06-15 00:38:09 +02:00
LICENSE.md Initial commit 2021-02-17 18:06:14 +01:00
README.md Add poetry installation step to README 2021-06-26 04:35:59 +02:00
pyproject.toml Replace tensorflow-io with biopython 2021-05-31 12:30:57 +02:00
shell.nix Add Tensorflow workarounds to shell.nix 2021-05-06 00:12:24 +02:00

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