VIRA: By-Reference Exon and CDS Viral Genome Annotation

Introduction

VIRA is a fully-automated protocol for transfering annotations from reference to target genomes, optimized for viral genomes and primarily developed and tested on HIV and SIV genomes.

The method uses both nucleotide and protein sequence information to search for correct alignments between genomes with high degrees of sequence divergence. VIRA is tailored to take advantage of guide protein annotations to further improve the accuracy of alignments and final annotations.

Publications

Coming soon...

Documentation

Installation

Via PyPI

The easiest way to install VIRA is through PyPI:

$ pip install vira-av
$ vira --help

To uninstall VIRA:

$ pip uninstall vira-av

Building from source

To build from source, clone the git repository:

$ git clone https://github.com/alevar/vira.git --recursive
$ cd vira
$ pip install -r requirements.txt
$ pip install .

Requirements

Getting started

Usage

vira [-h] -a ANNOTATION -g GENOME -t TARGET [-q GUIDE] [-o OUTPUT] [--force-cds] 
     [--gffread GFFREAD] [--minimap2 MINIMAP2] [--miniprot MINIPROT] [--snapper SNAPPER] 
     [--keep-tmp] [--tmp-dir TMP_DIR]

Options

Help Options

Example Data

Sample datasets are provided in the "example" directory to test and get familiar with VIRA.

The included example can be run with the following command from the root directory of the repository:

vira --annotation example/query.gtf --output example/output.gtf --genome example/query.fasta --target example/target.fasta --guide example/guide.gtf