GEN220: Highthroughput Biological Data Analysis - Fall 2026

See the Syllabus PDF for an overview of lecture topics.

Examples worked during class will be uploaded in this working repository. To check it out and keep it update.

git clone https://github.com/biodataprog/GEN220_2026_examples.git
cd GEN220_2026_examples
# ... time passes, new examples are uploaded
git pull # to get the latest version of the files

# let's also checkout the example datasets for the class
cd ..
git clone https://github.com/biodataprog/GEN220_data.git

Resources

• HPCC instructions on using SSH keys
• Access HPCC via web
• Git and GitHub guide and Software Carpentry Github Tutorial
• Software Carpentry UNIX/Shell Novice Tutorial
• UNIX command reference 1
• UNIX command reference 2
• Shell Scripting Tutorial
• Intro to Command-Line from HPCC

Major Topic Areas

• UNIX Shell scripting and using HPCC
• Python Programming
• Bioinformatics analysis methods
• Editors
  • VIM/VI
  • Nano
  • Emacs
  • Emacs Manual
  • Visual Studio - see HPCC INSTRUCTIONS - there is also a web-version you can run if you only have a tablet, the HPCC instructions will help set this up too.

Homework

• HW0 - Intro PDF
• HW1 - Unix PDF
• HW2 - Python 1 PDF
• HW3 - Python and BLAST PDF
• HW4 - AI Programming PDF
• HW5 - GitHub Website PDF

Project

• 2026 Project ideas 2026 Project Topics PDF
• Project Team Ideas PDF
• Project Team Report Template PDF
• Project Presentation Info PDF

Lectures

The course will be divided into three topic areas.

UNIX

1. UNIX I: Logging In and Command Line Basics PDF
2. UNIX II: Files, Data and Running Programs PDF
3. UNIX III: Shell Programming PDF
4. UNIX III Lab: Data Processing with Pipes PDF (lab / reading)
5. UNIX IV: Running Analyses on the Cluster PDF

Python

1. Python I: Values, Variables and Strings PDF
2. Python II: Decisions, Lists, Loops and Files PDF
3. Python III: Dictionaries, Sets, Tuples and Functions PDF
4. Python Workshop: Practice with Real Data PDF
5. Python IV: Modules, Packages and Biopython PDF
6. Python IV: Tables with Pandas PDF
7. Python V: Regular Expressions PDF
8. Python V: Regular Expressions Worked Examples PDF
9. Plotting Data with Python PDF

Bioinformatics and Genomics

1. Bioinformatics: Basics and BLAST PDF
2. Bioinformatics: Workshop - parsing data PDF
3. Bioinformatics: Short Reads PDF
4. Bioinformatics: Genomic Data Ranges PDF
5. Bioinformatics: RNASeq PDF
6. Bioinformatics: Variation and SNPs PDF
7. Bioinformatics: Workshop - SNPs per gene and splice sites PDF
8. Bioinformatics: Protein domains PDF
9. Bioinformatics: Orthology PDF
10. Bioinformatics: Workshop - orthologs and gene networks PDF
11. Bioinformatics: Phylogeny and Gene Families PDF
12. Bioinformatics: Sequence Evolution and Statistics PDF
13. Bioinformatics: Microbiome PDF
14. Bioinformatics: Genome Browsers PDF

Other skills and Tools

1. Plotting data with R and ggplot2 PDF - includes an R primer. Use RStudio on HPCC through OnDemand, Posit Cloud or install RStudio on your own computer. The same plots in Python are in Python: Plotting Data.
2. Building Websites using github.io PDF
3. Tabular data: CSV, Parquet and SQL with DuckDB PDF