DraVAR (Drug Resistance Associated VARiant detector) is a pipeline for analyzing genomic data to identify variants associated with drug resistance. The pipeline integrates tools for quality control, alignment, variant calling, annotation and gradation as per drug resistance association in Mycobacterium tuberculosis using statistical matrics.
Features
Automated variant calling and annotation.
Integrates widely used bioinformatics tools.
Flexible and customizable for different reference genomes and datasets.
Installation Install Dependencies
The pipeline requires the following software. Install them via conda:
conda create -n draVAR_env -c bioconda -c conda-forge \ fastqc trimmomatic bwa samtools bcftools freebayes snpeff vcfpy pandas conda activate draVAR_env
fastqc --version trimmomatic -version bwa samtools --version bcftools --version freebayes --version python -m vcfpy --help
Usage Input Files
The pipeline requires three input files:
Reference Genome (`ref.gb`): A GenBank file for the reference genome.
Read Files (`reads_1.fastq.gz` and `reads_2.fastq.gz`): Paired-end sequencing data.
Run the Pipeline
Run the pipeline with the following command:
sh DraVAR.sh --ref 'ref.gb' --R1 reads_1.fastq.gz --R2 reads_2.fastq.gz --prefix prefix --output out
Parameters
--ref: Path to the reference genome in .gb or .gbk format.
--R1: Path to the first paired-end read file (reads_1.fastq.gz).
--R2: Path to the second paired-end read file (reads_2.fastq.gz).
--prefix: Prefix for naming intermediate and result files.
--output: Directory to store the results.
Contribution
Feel free to fork the repository and submit pull requests to improve the pipeline.
For questions or issues, contact Ankita Pal at [email protected].
Example
DraVAR.sh --ref 'AL123456.gb' --R1 'reads_1.fastq.gz' --R2 'reads_2.fastq.gz' --prefix 'example' --output 'results'
You can also run using nextflow
nextflow run pipeline.nf --ref /path/to/reference.gb --reads1 /path/to/reads_1.fastq.gz --reads2 /path/to/reads_2.fastq.gz --prefix your_prefix --output_dir /path/to/output