This repository contains the source code and the trained model for De novo Error Correction for Nanopore RNA-seq Long Reads Using Deep Learning.
Download the source code and the trained model from this repository.
In addition, also install the following software packages and tools:
Keras-TensorFlow (v 2.8.0)
SPOA (v 4.0.7)
Pychopper (v1)
cutadapt (v 3.5)
isONclust (v 0.0.6.1)
Modify the directory paths (bin_dir) accordingly in the code of this repository (several .py and .sh files), to point to your local directory that holds the source code of this repository and your local directories that hold the executables of the corresponding software tools.
The neural network model trained with ONT RNA-seq (cDNA) data is available under the model/ directory (trained_model/) in this repository.