VIDHOP

VIDHOP is a virus host predicting tool. Its able to predict influenza A virus, rabies lyssavirus and rotavirus A.

Install:

We recommend to use miniconda for the enviroment management

1. Download and install Conda.

2. Create a Conda environment with a Python 3.6 or higher

   conda create -n epidope python=3.7

3. Activate the Conda environment. You will need to activate the Conda environment in each terminal in which you want to use epidope.

   conda activate vidhop

4. Install vidhop via conda

   conda install -c flomock -c conda-forge vidhop

How to use:

First, if have not already activated your conda environment:

conda activate vidhop

now you can simply use vidhop via:

Example:

  $ vidhop -i /home/user/fasta/influenza.fna -v influ

present only hosts which reach a threshold of 0.2

  $ vidhop -i /home/user/fasta/influenza.fna -v influ -t 0.2

if you want the output in a file

  $ vidhop -i /home/user/fasta/influenza.fna -v influ -o /home/user/vidhop_result.txt

use multiple fasta-files in directory

  $ vidhop -i /home/user/fasta/ -v rabies

use multiple fasta-files in directory and only present top 3 host predictions per sequence

  $ vidhop -i /home/user/fasta/ -v rabies -n_hosts

Options:

command	what it does
-i, --input	either raw sequences or path to fasta file or directory with multiple files. [required]
-v, --virus	select virus species (influ, rabies, rota) [required]
-o, --outpath	path where to save the output
-n, --n_hosts	show only -n most likely hosts
-t, --thresh	show only hosts with higher likeliness then --thresh
--auto_filter	automatically filters output to present most relevant host
--help	show this message and exit.
--version	show version number from vidhop

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.