This course is suited for beginners in Bioinformatics with very little prior knowledge. Its objective is to teach scientists working with NGS data the basic skills to write their own Python scripts to handle their data.
The course will be focused on direct application of the learned techniques in hands-on labs. Basic knowledge of working with the command line is advantageous, but not a prerequisite.



In order to prepare your computer for the course please follow this guide and afterwords test your Python setup with these scripts: Windows and Linux/MAC.

If you have any questions or problems please write an email to Felix Heeger.

Day 1 (Monday)

Chapter 1: Text output and manipulation


Solutions: ex1-1 ex1-2 ex1-3 ex1-4 ex1-5

Chapter 2: Reading and writing files


Exercise: genomic_dna.txt

Solutions: ex2-1 ex2-2 ex2-3

Day 2 (Tuesday)

Chapter 3: Lists and loops


Exercise: ex3-1_input.txt ex3_genomic_dna.txt exons.txt

Solutions: ex3-1 ex3-2

Chapter 4: Writing your own functions


Solutions: ex4-1 ex4-2

Day 3 (Wednesday)

Chapter 5: Conditional statement


Exercises: data.csv

Solutions: ex5-1 ex5-2

Chapter 6: Dictionaries


Exercises: dna.txt translation.txt

Solutions: ex6-1

Day 4 (Thursday)

Chapter 7: Files, programs and user input



Solutions: ex7-1 ex7-2

Chapter 8: Biopython


Exercise: sample1.fq reads.fq

Solutions: ex8-1 ex8-2 (Note: ex8-2 was not done during the course)

Day 5 (Friday)

Hands on training on participant problems

  1. Sub-sampling NGS reads
    Solution: subsampling
  2. Determining sequence frequency in NGS data
    Solution: sequenceFrequency
  3. Finding orthologous proteins between different bacteria