Practical Linux, Bash, AWK, Python, Git, and HPC scripting exercises developed for MSc Bioinformatics systems training.
Build operational command-line proficiency for real-world bioinformatics workflows: data parsing, automation, job submission, and reproducible scripting habits.
- Bash control flow and scripting patterns
- Text processing with AWK
- Basic Python scripting for data handling
- BLAST command-line usage and result filtering
- Linux shell fluency and file-system operations
- Git command workflow essentials
- HPC execution concepts (Eddie job usage notes)
Representative files include:
- loop/variable scripting examples (
bash_loops.sh,bash_variables.sh) - Bash↔AWK integration (
bash_to_awk.sh,myawkscript.awk) - BLAST examples and post-processing (
blast.sh,good_or_bad_BLAST.sh) - HPC cheat sheet (
eddie.sh) - Git usage notes (
git_cheatsheet.md)
This repository highlights foundational systems skills required by bioinformatics roles:
- Unix-first working style
- script-based automation
- reliable command-line data processing
- environment readiness for pipeline and HPC work