Bioinfo-Utils: Linux & Bash for NGS 🧬

A curated collection of Bash scripts and Linux commands optimized for Next-Generation Sequencing (NGS) data processing.

🌟 Why this exists

In bioinformatics, we spend 80% of our time "wrangling" data. These scripts automate the repetitive parts of the pipeline, from file management to HPC job submission.

🛠️ Included Tools

1. Batch Renaming: Clean up messy sequencing provider names.
2. Automated QC: One-command FastQC/MultiQC wrapper.
3. Region Extractor: Fast extraction of genome coordinates using bedtools.
4. SLURM Template: Best-practice template for cluster job submission.

📂 Usage

Ensure scripts have execution permissions:

chmod +x scripts/*.sh
./scripts/batch_rename.sh ./data fastq.gz SAMPLE_A