A comprehensive pipeline for the genomic analysis of Ebola virus, the causative agent of Ebola virus disease
EboGen is a modular and automated pipeline designed to simplify and standardize the genomic analysis of Ebola Virus. It integrates quality control, variant calling, consensus genome generation, clade typing, and phylogenetic analysis into a streamlined workflow.
- Quality Control: Automatically cleans and filters raw sequencing reads to ensure data accuracy.
- Variant Calling: Accurately identifies SNPs and indels using GATK, providing enhanced genomic insights.
- Consensus Genome Generation: Produces high-quality, reference-based genome assemblies for downstream analysis.
- Phylogenetic Analysis: Generates robust phylogenetic trees using maximum likelihood and neighbor-joining methods.
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/EboGen.git
cd EboGen
conda env create -n EboGen --file EboGen_installer.yml
bash setup.sh
Run the program to make sure you have access to all the plug-ins using the command EboGen -h to view output below:
This is EboGen $version
Developed and maintained by Stephen Kanyerezi, Ivan Sserwadda, & Gerald Mboowa
Synopsis:
EboGen is a modular and automated pipeline designed to simplify and standardize the genomic analysis of Ebola Virus. It integrates quality control, variant calling, consensus genome generation, and phylogenetic analysis into a streamlined workflow.
Usage:
Given paired reads, to perform variant calling and generate a consensus genome; EboGen [options] -R1 <path of forward read> -R2 <path of reverse read> -o <output directory to be created> --varcall true
Given a multifasta file, to perform phylogeny; EboGen [options] --multifasta <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:
-R1/--forward-read Path of the forward reads [either .fastq or .fastq.gz]
-R2/--reverse-read Path of the reverse reads [either .fastq or .fastq.gz]
--multifasta Path of mulitfasta file. Applicable if you want to perform phylogenetics
-o/--output-dir Directory to be created for results
--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
If you want to perform variant calling and consensus genome generation only, run the command below
EboGen -o <output_dir> -R1 <forward read path> -R2 <reverse read path> --varcall true
If you have a multi fasta file and you want to perform phylogenetics, run the command below
EboGen -o <output_dir> --multifasta <path to multi fasta file> --phylogeny true
Here we describe the output files generated from the analysis pipeline. The outputs are organized into different directories based on their function.
| Directory | File(s) | Description |
|---|---|---|
| alignment/ | BAM File | Contains the aligned sequencing reads, used for downstream variant calling and consensus genome generation. |
| 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 |