Introduction to Plasmodium Genomics

This tutorial outlines the basics concepts in Plasmodium genomics, specifically in relation to detecting drug resistance *Please note that this is a rapidly evolving field and one currently with limited easy to use bioinformatics approaches. The slides and worksheets here are only meant to serve as examples of approaches which need constant updating and checking.
Much to the material provided on this page was generated from material generously provided by Dr. Eline Kattenberg, Institute of Tropical Medicine, Belgium

Learning outcomes

Classify Plasmodium species, specifically those that infect humans
Describe the genetic structure of Plasmodium across the three structures
Compare amplicon and genome sequencing approaches
Describe linkage disequilibrium and its uses in Plasmodium epidemiology
Recognise the key genes involved in Plasmodium drug resistance
State the primary data types and computational approaches for determining Plasmodium population structure
Run simple analysis of WGS data using malaria-profiler

It is recommended that you have Notepad++ (Windows) or BBEdit (Mac) for viewing fasta files; most linux default editors can do this.
It is recommended that you have followed the Concepts in Computer Programming, UNIX tutorial (basics) and Setting up and using conda tutorials if you are going to do the Malaria-profiler worksheet.

Please do the pre-learning quiz, then watch the presentation.
Once finished the tutorial, take the post-learing quiz.

The malaria-profiler tool outlined in this worksheet is still under active development and is in early stages of use. Please do not use this tool yet for reliable analyses
This tool works best when it has an extensive library of drug resistance and population structure markers. If you know of one not in the associated database please contact the developer