kartzz/pipeline repository overview

NGS Pipeline Docker Image This Docker image provides a fully configured environment for running end-to-end NGS data analysis pipelines, including quality control, alignment, and downstream processing.

Features Pre-installed bioinformatics tools:

bwa

samtools

bcftools

fastqc

fastp

multiqc

Supports multi-threading

Ready for automation and batch processing

Compatible with cloud and Kubernetes workflows

Pull Image docker pull kartzz/pipeline:latest Run Container docker run -it --rm
-v $(pwd):/data
kartzz/pipeline:latest
bash

1. Quality Control fastqc /data/sample.fastq
2. Trimming fastp -i /data/sample.fastq -o /data/clean.fastq -w 4
3. Alignment bwa mem -t 4 ref.fa /data/clean.fastq > /data/aligned.sam
4. Convert & Sort samtools view -Sb /data/aligned.sam | samtools sort -o /data/aligned.bam
5. Variant Calling bcftools mpileup -f ref.fa /data/aligned.bam | bcftools call -mv -o /data/variants.vcf
6. Generate Report multiqc /data