Learning resources

Tutorials, workshops and seminars

To do bioinformatics well, you need to learn 3 things. The Unix shell (command line), a scripting language like Python (or Perl if you must), and the stats environment R. All are free, can be learnt online for free. Once you’ve learnt these things, you will be able to do pretty much anything in terms of bioinformatics analysis, including reading and parsing data files, analysing and plotting data, and making your own analysis pipelines.

Unix

Python

  • Beginners: Non-programmer’s tutorial for Python by Josh Cogliati (PDF)
  • Beginners: Python & programming trainig with Rosalind
  • Beginners: Learn programming with Python (Coursera); check for new courses on Coursera too
  • Some coding experience: Python tutorials from ANGUS
  • Some coding experience: A primer on Python
  • Some coding experience: Python intro talks on Software Carpentry (assumes basic programming concepts like variables, loops, conditionals, lists/arrays)
  • Reference: PythonQuick – handy tutorial & reference for Python
  • Reference: BioPython Tutorial – a Python package providing modules for common tasks in bioinformatics, including reading and writing sequence data
  • Reference: BioPython wiki – examples on how to use some modules

Next Gen sequencing analysis

Phylogenetics – also see software page

Phylogenetics in R

Primers for people trained in computer science, maths or stats:

Papers & seminars introducing sequencing & next generation sequencing

ECCB 2010 Next-gen sequencing Tutorial (Thomas Keane@Sanger)

Other slides from Thomas Keane

Bacterial genomics

More Phylogenetics Methods

Useful sources of information

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