Welcome to Stellenbosch University


​​Introduction to Python for Bioinformatics

This short course gives biologists with little background in coding computer programs an introduction to Python 3.  After completion of this course you should be able to code functional Python programs to use in your research.  Emphasis is placed on topics that are relevant to bioinformatics. The course is presented as a series of annotated PowerPoint presentations. This course makes use of Python 3.6​ and PyCharm Community Edition​ 2017.3.2.

Introduction to Python for Biologists V3_8.pdf

1. Data Structures (12 min).pptx 

2. Variables Operators and Strings (31 min).pptx 

3. Lists, Tuples, Sets and Dictionaries (44 min).pptx

4. Data Input and Output (60 min).pptx

5. Loops and Enumeration (64 min).pptx

6. Conditional statements (18 min).pptx

7. Functions, scope and recursion (54 min).pptx

8. Classes, OOP and iteration (45 min).pptx

9. Modules, numpy and ndarray (43 min).pptx

10.Exceptions (14 min).pptx

11.Debugging (16 min).pptx

Introduction to Bioinformatics


Pairwise alignment.pdf


Multiple Sequence Alignment.pdf

Hidden Markov Models.pdf


A slideset used at the workshop on the ChIP-seq technique: ChIP_seq Workshop 22 June 2016 final.pdf

High Performance Cluster

HPC wiki


Introduction to Matplotlib.pdf

Genome Assembly Workshop

  1. Linux and HPC.pdf
  2. Introduction to NGS.pdf
  3. Introduction to FastQC.pdf
  4. Genome Assembly.pdf
  5. SPAdes.pdf
  6. QUAST and bandage.pdf
  7. PacBio.pdf