kartzz/ngspipeline repository overview

NGS Pipeline Docker Image

A ready-to-use Docker image for running Next-Generation Sequencing (NGS) analysis pipelines in a reproducible, scalable, and portable environment.

This image bundles commonly used bioinformatics tools and dependencies required for end-to-end genomic data processing, eliminating the need for complex local installations.

🚀 Features 🧪 Preconfigured environment for NGS workflows 📦 Includes essential bioinformatics tools and dependencies 🔁 Reproducible and portable execution across systems ⚡ Optimized for performance and pipeline automation 🐳 Easy integration with Docker-based workflows and CI/CD 📦 Use Cases Whole genome / exome sequencing analysis RNA-Seq data processing Variant calling pipelines Quality control and preprocessing of sequencing data Bioinformatics workflow automation 🛠️ Getting Started Pull the Image docker pull kartzz/ngspipeline:latest Run the Container docker run -it --rm kartzz/ngspipeline:latest Mount Local Data docker run -it --rm
-v $(pwd)/data:/data
kartzz/ngspipeline:latest ⚙️ Pipeline Components

Typical tools and utilities included (may vary by tag):

Quality control (e.g., FastQC) Read trimming and filtering Alignment tools (e.g., BWA, Bowtie2) SAM/BAM processing (e.g., SAMtools) Variant calling tools Python/R environments for downstream analysis 📁 Directory Structure Path Description /data Input/output data directory /tools Installed bioinformatics tools /scripts Pipeline scripts 🔄 Workflow Integration

This image can be used with:

Docker Compose Workflow managers (Nextflow, Snakemake) Kubernetes-based pipelines CI/CD pipelines for bioinformatics automation 🧩 Customization

You can extend this image by:

Adding additional tools Modifying pipeline scripts Installing custom dependencies

Example:

FROM kartzz/ngspipeline:latest

RUN apt-get update && apt-get install -y