Bioinformatics often involves working with massive sequencing datasets (e.g., FASTQ, BAM, VCF) and requires chaining together dozens of command-line tools. Knowing Bash allows us to:

• Automate analysis pipelines
• Filter, clean, and transform large datasets
• Manage files, permissions, and job scripts in HPC environments
• Work smoothly on remote servers and cloud platforms via SSH

Tutorial1 (tutorial1.ipynb) covers the fundametal concepts:

• File system navigation (cd, ls, pwd)
• Permissions & ownership (chmod, chown)
• Script creation and execution
• Finding files and managing users (find, id, dscl)

Tutorial2 (tutorial2.ipynb) discusses the awk tool

Tutorial3 (tutorial3.ipynb) discusses the grep tool

Requirements

• macOS or Linux environment (or WSL on Windows)
• Jupyter Notebook or VS Code