vira-av 1.0.0

VIRA: By-Reference Exon and CDS Viral Genome Annotation

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

Requirement	Details
Language support	Python ≥ 3.6
Dependencies	- gffread - minimap2 - miniprot - snapper

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

Option	Description
-a, --annotation	Path to the query GTF/GFF annotation file.
-g, --genome	Path to the query genome FASTA file.
-t, --target	Path to the target genome FASTA file.
-q, --guide	Optional path to the guide annotation file for the target genome. Transcripts and CDS from the guide will be used to validate the annotation.
-o, --output	Path to the output GTF file.
--force-cds	Force the CDS from the guide onto the transcript chain, even if that means merging adjacent exons together (can fix alignment artifacts such as spurious introns). If the CDS does not fit the transcript chain, the transcript will be skipped.
--gffread	Path to the gffread executable.
--minimap2	Path to the minimap2 executable.
--miniprot	Path to the miniprot executable. If not set - minimap2 will be used to align nucleotide sequence of the CDS instead.
--snapper	Path to the snapper executable.
--keep-tmp	Keep temporary files.
--tmp-dir	Directory to store temporary files.

Help Options

Option	Description
-h, --help	Prints help message.

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