Genome Sequencing Bioinformatics - Africa

Call for Classroom Hosts:

This is a call for Hosts interested in hosting a classroom for local participants for a pan-African sequencing bioinformatics course. Classroom Hosts help facilitate the course by supervising participants as they work through the course content.

Host prerequisites:

• Have the will to supervise and support local participants as they work through the course
• Have experience in use of the Bash command language  for bioinformatics tasks
• Have access to a computer with at least an i5 or equivalent processor, 8GB RAM, and 100GB of disk space (note, M1 Macs are not suitable)
• Be able to recruit systems administrators and teaching assistants to aid them in running of their classroom

Course Summary: 

In collaboration with H3ABioNet, we are pleased to announce the next iteration of the Genome Sequencing Bioinformatics Africa course.

High throughput sequencing is an essential tool in genetic and genomic analysis. It is increasingly important for experimental scientists to gain the bioinformatics skills required to analyse the large volumes of data produced by sequencers. This course will equip participants with the essential informatics skills required to begin analysing sequencing data and apply some of the most commonly used tools and resources for sequence data analysis. 

The programme will cover prominent sequencing technologies, algorithmic theory and principles of bioinformatics, with a strong focus on practical computational sessions using sequence analysis techniques and tools applicable to any species or genome size. A variety of applications will be covered from post-sequencing analysis, quality control, alignment, assembly, and variant calling.

This course will apply a blended learning format consisting of locally coordinated classrooms referred to as “distributed classrooms”. See the publications by Gurwitz et al. and Ras et al for more information. The local classrooms for this course may run virtually using Zoom.

Time commitment:

Contact sessions will run on Tuesdays and Thursdays lasting for 4 hours per session.

Target audience:

The course is aimed at postdoctoral scientists, senior PhD students, junior faculty members or clinicians/healthcare professionals based in Africa who are actively engaged in or soon to commence research involving  sequencing data analysis.

Please note:

The practical sessions will be taught exclusively through Unix/Linux. Therefore, participants are required to have some previous experience using the Linux operating system. This will be essential for participants to fully benefit from the course. There are numerous online introductory tutorials to the UNIX/Linux operating system and command line, including:
http://www.ee.surrey.ac.uk/Teaching/Unix 
http://swcarpentry.github.io/shell-novice/  

The course will run for 10 weeks on Tuesdays and Thursdays (4 hours per session) from 15 Aug–10 October 2023

The programme will cover the following core topics:

• Intro to Unix/Linux & running workflows
• Introduction to Sequencing Technologies
• Sequencing data pre-processing and QC
• Alignment to reference sequences
• Variant calling and annotation

Learning outcomes
On completion of the course, participants should expect to be able to:

• Use the unix command-line as a tool for data analysis
• Describe the different sequencing data file formats available
• Perform QC assessment of high throughput sequencing data
• Explain the algorithmic concepts behind read alignment, variant calling and structural variant detection
• Perform read alignment, variant calling and structural variation detection using standard tools
  

Host prerequisites:

Classroom Hosts help facilitate the course by supervising participants as they work through the course content. Hosts and their staff (teaching assistants + system administrators) are in each classroom with the participants for watching video lectures and practical activity (either in person or in virtual breakout rooms). All classrooms link up for contact sessions with the instructor for a given module.

Hosts must be comfortable with unix command line for bioinformatics. The primary coding language to be used is Bash.  

Hosts also appoint system administrators and teaching assistants for their classroom. Participants then apply for the course indicating the nearest classroom to them. Hosts decide whether to have a physical classroom or if their participants will meet in a virtual breakout room. Coordination of the various teams and participants is managed with a learning management system. 

To apply to host a classroom, use the “Apply” button above

The course is subsidised by Wellcome Connecting Science Courses and Conferences.

Feedback from 2022 course

“I enjoyed the interactions on zoom and vula, the facilitators and the teaching assistants were great. I am grateful for the exposure. Everyone was pleasant and explained concepts as easily as they could.”

“Honestly, I liked everything about the course from the beginning to the end. It was very rich in information and the quality of the teaching was good, I really enjoyed doing the assignments.”