🎬 VaricellaGen

A comprehensive pipeline for the genomic analysis of Varicella-zoster virus (VZV), the causative agent of chickenpox.

🏆 About

VaricellaGen is a modular and automated pipeline designed to simplify and standardize the genomic analysis of Varicella-zoster virus (VZV). It integrates quality control, variant calling, consensus genome generation, clade typing, and phylogenetic analysis into a streamlined workflow.

🏷️ Key Features:

1. Quality Control: Automatically cleans and filters raw sequencing reads to ensure data accuracy.
2. Variant Calling: Accurately identifies SNPs and indels using GATK, providing enhanced genomic insights.
3. Consensus Genome Generation: Produces high-quality, reference-based genome assemblies for downstream analysis.
4. Clade Typing: Rapidly classifies VZV isolates into established clades.
5. Phylogenetic Analysis: Generates robust phylogenetic trees using maximum likelihood and neighbor-joining methods.

⚙️ Installation

Make sure you have Miniconda or Anaconda on your Linux system using the links provided Clone the software from the offical repository using:

conda activate base

cd && git clone https://github.com/MicroBioGenoHub/VaricellaGen.git

cd VaricellaGen

conda env create -n VaricellaGen --file VarGen_installer.yml

bash setup.sh

Run the program to make sure you have access to all the plug-ins using the command VaricellaGen -h to view output below:

This is VaricellaGen $version
Developed and maintained by Stephen Kanyerezi, Ivan Sserwadda, Jupiter Marina Kabahita, & Gerald Mboowa

Synopsis:
        VaricellaGen is a modular and automated pipeline designed to simplify and standardize the genomic analysis of Varicella-zoster virus (VZV). It integrates quality control, variant calling, consensus genome generation, clade typing, and phylogenetic analysis into a streamlined workflow.

Usage: 
        Given paired reads, to run perform variant calling, clade typing and consensus genome generation; VaricellaGen [options] -f <path of forward read> -r <path of reverse read> -o <output directory to be created> --typing true
        Given paired reads, to perform variant calling and generate a consensus genome without clade typing; VaricellaGen [options] -f <path of forward read> -r <path of reverse read> -o <output directory to be created> --varcall true
        Given a multifasta file, to perform phylogeny; VaricellaGen [options] --consensus <path of multifasta file> --phylogeny true -o <output directory to be created> 

General:
        -h/--help       Show this help menu
        -v/--version    Print version and exit
        -x/--citation   Show citation and exit

Mandatory options for paired reads:
        -f/--forward-read       Path of the forward reads [either .fastq or .fastq.gz]

        -r/--reverse-read       Path of the reverse reads [either .fastq or .fastq.gz]

        --consensus             Path of mulitfasta file. Applicable if you want to perform phylogenetics

        -o/--output-dir         Directory to be created for results

        --typing                 [true or false (default)] Run the pipeline to generate variants, clade typing, and consensus genome.

        --varcall               [true or false (default)] Genrate variants and consensus genome only.

        --phylogeny             [true or false (default)] construct a phylogenetic tree. Applicable only with --consensus option and if --varcall and --typing not set to true

Other options:

        --cores                 Number of cpus to use. Default=16
                     
For further explanation please visit: https://github.com/MicroBioGenoHub/VaricellaGen

How ro Run

If you want to perform variant calling, consensus genome generation, and clade typing, run the command below

VaricellaGen -o <output_dir> -f <forward read path> -r <reverse read path> --typing true

If you want to perform variant calling and consensus genome generation only, run the command below

VaricellaGen -o <output_dir> -f <forward read path> -r <reverse read path> --varcall true

If you have a multi fasta file and you want to perform phylogenetics, run the command below

VaricellaGen -o <output_dir> --consensus <path to multi fasta file> --phylogeny true

Output Files

Here we describe the output files generated from the analysis pipeline. The outputs are organized into different directories based on their function.

Directory Structure

Directory	File(s)	Description
alignment/	BAM File	Contains the aligned sequencing reads, used for downstream variant calling and consensus genome generation.
clade/	clade.csv	CSV file with a header row, followed by sequence IDs and their corresponding clades, used for phylogenetic classification.
consensus/	Consensus FASTA File	Contains the final consensus genome sequence.
	Metrics File	Reports genome coverage and N-content statistics.
qc/	HTML Files	Contain quality control (QC) reports.
	trimmed_fastq/	A subdirectory containing trimmed FASTQ files after quality filtering and adapter removal.
variants/	GVCF File	Stores variant calls in genomic variant call format (gVCF).
	Decomposed VCF File	A normalized version of the variant call file.
	Fixed & Ambiguous VCF Files	Processed VCF files having fixed and ambiguous variants.
	mask.txt	A text file listing masked regions in the consensus genome.
phylogeny/	msa	A subdirectory containing an MSA file
	tree	A subdirectory containing the nexus tree