kartzz/ngs-bio repository overview

Title: NGS Bioinformatics Pipeline Docker Image

Short Summary: Containerized pipeline for RNA-Seq and DNA-Seq processing with BWA, HISAT2, Bowtie2, Samtools, BCFTools, FastQC, fastp, MultiQC, and SRA Toolkit on Ubuntu 22.04. Includes reference genome indexing and automated variant calling.

Steps / Features:

Base Image: Uses Ubuntu 22.04 LTS for stability. Dependency Installation: Installs essential bioinformatics tools: bwa, hisat2, bowtie2, samtools, bcftools, fastqc, fastp, multiqc, sra-toolkit. Installs system utilities (wget, curl, unzip, gzip) and Python 3/JRE. Certificate & OpenSSL Updates: Updates CA certificates for secure downloads. Directory Setup: Creates /data for input/output and /app/scripts for pipeline scripts. Optional bioinfo user created for non-root execution. Reference Genome Preparation: Downloads GRCh38 reference genome from Ensembl. Generates indices for BWA, HISAT2, Bowtie2. Automated NGS Pipeline (pipeline.sh): Downloads SRA datasets (SRR22044200, SRR22044199). Compresses FASTQ files using pigz. Performs quality check with FastQC. Trims reads with fastp. Aligns reads using HISAT2, Bowtie2, and BWA MEM. Converts SAM → BAM, sorts, and indexes using Samtools. Calls variants with BCFTools. Generates MultiQC report summarizing all QC metrics. Execution: Pipeline is executable with /app/scripts/pipeline.sh. Default command runs this script automatically.

Usage Example:

docker run --rm -v /local/data:/data kartzz/ngs-bio:tagname Mount your local data folder to /data in the container. Adjust THREADS environment variable if needed for parallel processing.

Benefits:

Fully reproducible, containerized bioinformatics workflows. Ready-to-run with minimal setup. Supports multiple aligners and automated QC & variant calling.