--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Wed Nov 09 12:19:26 2022 +0000
@@ -0,0 +1,90 @@
+# VirHunter
+
+VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequening datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host and bacterial (contamination).
+
+## System Requirements
+VirHunter installation requires a Unix environment with [python 3.8](http://www.python.org/). 
+It was tested on Linux and macOS operating systems. 
+For now, VirHunter is still not fully compatible with M1 chip MacBook.
+
+In order to run VirHunter you need to have git and conda already installed. 
+If you are installing conda for the first time, we suggest you to use 
+a lightweight [miniconda](https://docs.conda.io/en/latest/miniconda.html).
+Otherwise, you can use pip for the dependencies' installation.
+         
+## Installation 
+
+To install VirHunter, you need to download it from github and then to install the dependancies.
+
+First, clone the repository from [github](https://github.com/cbib/virhunter)
+
+git clone https://github.com/cbib/virhunter.git
+
+Go to the VirHunter root folder
+
+cd virhunter/
+
+### Installing dependencies with Conda
+
+First, you have to create the environment from the envs/environment.yml file.
+The installation may take around 500 Mb of drive space. 
+
+conda env create -f envs/environment.yml
+
+Second, activate the environment:
+
+conda activate virhunter
+
+### Installing dependencies with pip
+
+If you don't have Conda installed in your system, you can install python dependencies via pip program:
+
+pip install -r envs/requirements.txt
+
+Then if you have macOS you will need to install wget library to run some scripts (Conda installation already has it). You can do this with brew package manager.
+
+brew install wget
+
+### Testing your installation of VirHunter
+
+You can test that VirHunter was successfully installed on the toy dataset we provide. 
+IMPORTANT: the toy dataset is intended only to test that VirHunter has been well installed and all the scripts can be executed. 
+These modules should not be used for prediction on your owd datasets!
+
+First, you have to download the toy dataset
+
+bash scripts/download_test_installation.sh
+
+Then run the bash script that calls the testing, training and prediction python scripts of VirHunter.
+Attention, the training process may take some time (up to an hour).
+
+bash scripts/test_installation.sh
+
+
+## Using VirHunter for prediction
+
+To run VirHunter you can use the already pre-trained models or train VirHunter yourself (described in the next section).
+Pre-trained model weights are already available for the multiple host plants. 
+You can download them using the download_weights.sh script.
+
+bash scripts/download_weights.sh
+
+Once the config file is ready, you can start the prediction:
+
+python virhunter/predict.py --test_ds /path/to/test_ds_1
+
+After prediction VirHunter produces two csv files and one optional fasta file:
+
+1. The first file ends with _predicted_fragments.csv
+It is an intermediate result containing predictions of the three CNN networks (probabilities of belonging to each of the virus/plant/bacteria class) and of the RF classifier for each fragment of every contig.
+
+2. The second file ends with _predicted.csv.
+This file contains final predictions for contigs calculated from the previous file. 
+   - id - fasta header of a contig.
+   - length - length of the contig.
+   - # viral fragments, # plant fragments and # bacterial fragments - the number of fragments of the contig that received corresponding class prediction by the RF classifier.
+   - decision - class given by the VirHunter to the contig.
+   - # viral / # total - number of viral fragments divided by the total number of fragments of the contig.
+   - # viral / # total * length - number of viral fragments divided by the total number of fragments of the contig multiplied by contig length. It is used to display the most relevant contigs first.
+
+3. The fasta file ends with _viral.fasta. It contains contigs that were predicted as viral by VirHunter.