Key Dates

The course will run for 8 weeks with whole-day workshops every Wednesday from June 7th to July 26th, 2023.

Application deadline: May 12th, 2023

Course objectives

The goal of this course is to introduce some practical techniques for the analysis of genomic data for surveillance of Anopheles mosquitoes. At the end of the course, trainees will be able to:

• Perform a range of analyses on Anopheles genomic data that are relevant to malaria vector surveillance
• Describe key biological concepts underpinning the analyses
• Describe key computing technologies used for the analyses
• Interpret analysis results and discuss implications for malaria vector control policy

Course curriculum

The training course comprises 8 workshops, covering the following topics:

• Workshop 1 – Pyrethroid target-site resistance
• Workshop 2 – Metabolic insecticide resistance and copy number variation
• Workshop 3 – Population structure
• Workshop 4 – Cryptic species
• Workshop 5 – Genetic diversity
• Workshop 6 – Detecting genes under recent positive selection
• Workshop 7 – Gene flow and the spread of insecticide resistance
• Workshop 8 – Analysis planning and reporting

Trainee profile and requirements

This free course is aimed at scientists and public health professionals working in the field of malaria vector surveillance and control and meeting the following requirements.

• This is a hands-on training course. Trainees will require some prior experience of data analysis using scientific programming such as Python, R, Julia or Stata. The course will be conducted using the Python programming language.
• Data analysis will be performed using cloud computing services which can be accessed via a Web browser. Trainees will require access to a personal computer with a Web browser and stable internet connection.
• The training workshops will be designed to complement each other, building up a series of analytical skills and progressively introducing biological concepts and computing tools throughout the course. Trainees should ideally be in a position to complete the full course of 8 workshops.

Workshop format

Each training workshop will last approximately 6 hours, and will be delivered online via Zoom and Slack. The training will combine lectures and hands-on data analysis practical sessions in roughly equal proportion. Practical sessions will use cloud computing services and analyse real genome variation data on Anopheles gambiae mosquitoes. Practical sessions will be conducted in small groups with teaching assistants to provide support and answer questions.

For any further information and questions, please contact Paballo Chauke <pc24@sanger.ac.uk>

Application Form: https://forms.gle/sCYp3Wfc7sRqiPdF9