What will we cover over the next three weeks and who are your educators?

What are the next three weeks about?

In Week 1 of the course, we will introduce you to the concept of environment variables and demonstrate how to install key bioinformatics tools. We will talk about next-generation sequencing, its significance and different file formats used. We will describe different steps in a next generation pipeline ranging from sequence quality control, mapping and variant calling. We will show you how to run different commands on the UNIX command line for sequence quality control, mapping, and variant calling.

In Week 2 we will introduce you to the concepts of workflows and workflow management systems such as Nextflow. We will demonstrate how pipelines developed with Nextflow can perform the same types of tasks we outlined in Week 1 without you having to run each of the individual commands yourselves.

You will be shown how to install Nextflow and use the existing viralrecon pipeline from the nf-core project. You will set up a samplesheet to be used as input for viralrecon and then run the pipeline yourselves. Finally, we will examine the outputs from viralrecon and explain how these could be used to decide whether the data we analysed was of sufficient quality for downstream analyses.

In Week 3, following a good understanding of the analysis procedures you acquired in Week 1 and Week 2, we proceed with data visualization of variants obtained from genomic data.

We will use R and RStudio, tools that make it possible to use either built-in functions of R, or specific functions from packages for several purposes that greatly help when analyzing variants. In order to do achieve this, you should be knowledgeable about R data structures, how to provide statistical information on data, how to subset it, and how to visualize it – we will cover that during the week. We also cover examples of data types to represent, why we would do that, and how to quickly interpret it.

Help areas

You can leave your questions and comments all the way along the course. Towards the end of each week, there will also be a dedicated Help area for that week, please use that step to leave questions if you need help, your educators and your fellow learners might be able to help.

Help areas:

Week 1

Week 2

Week 3

Meet your Educators

We, your Educators on this course, will be present during the next three weeks of the course, following and joining in the discussions from time to time and sharing our expertise with you. On this journey together, we will be helping each other to learn. We will also be looking at your feedback, which will serve to improve the course.

At the end of each week, we provide a written summary of the week’s learning. We will also email you with a round-up of the week’s learning. We are looking forward to learning with you.

Ruth Nanjala

Educator and Developer

Ruth Nanjala is a computational scientist working on the genetics of the Human Leukocyte Antigen (HLA) region and its relationship to complex immune-mediated diseases such as Rheumatoid arthritis. She hopes to work towards addressing the gap in disease diagnosis, prognosis and treatment and thus address health challenges in Africa and beyond.

Ruth graduated with a distinction for the M.Sc. in Bioinformatics at Pwani University, Kenya and the University of Cape Town, South Africa. She holds a first-class B.Sc. degree in Microbiology from Pwani University, Kenya. She is currently pursuing a DPhil in Cellular and Molecular Medicine at the University of Oxford.

Ruth is also passionate about capacity building and has been involved with different projects aimed at building Bioinformatics capacity in Africa. These include the Pan African Bioinformatics network (H3ABioNet) and the Bioinformatics mentorship and incubation program at the International Centre for insect physiology and ecology (ICIPE).

Andries Van Tonder

Educator and Developer

A postdoctoral researcher at Department of Veterinary Medicine, University of Cambridge, with extensive experience in Mycobacterial genomics. The primary focus of my research is investigating the transmission dynamics of various bacterial species including Mycobacterium bovis in a multi-host system and non-tuberculous Mycobacteria in a hospital setting. Alongside my research I also have an interest in developing reproducible bioinformatics workflows using state of the art tools such as Nextflow.

Fatma Guerfali

Lead Educator and Developer

Fatma is a Researcher based at Institut Pasteur de Tunis, and Trainer in bioinformatics. Fatma is interested in engaging efforts to conduct research activities and participating in projects addressing Global Health threats. As such, she developed a complementary expertise in Biology and Bioinformatics that includes collecting and analysing pathogen isolates from patients, studying pathogens’ genome plasticity, and deciphering Omics-based signatures to identify biomarkers of the host-pathogen interplay. She actively shared this expertise by participating in setting up specific courses to leverage students’ skills in bioinformatics. She is a member of international capacity-building projects such as H3ABioNet and PHINDaccess.

Dusanka Nikolic

Education Developer

Dusanka’s background is both in Computer Science and Education. In her present role as Senior Education Developer, Dusanka focuses on research-based design and development of MOOCs within the Wellcome Connecting Science (WCS) digital learning programme. She coordinates, leads and co-leads teams of experts, developers and educators on the online courses, providing pedagogical guidance and mentorship.

Dusanka develops interactive exercises for the online courses to enhance online learning of subjects typically taught face-to-face. She also takes part in teaching of education modules in face to face or hybrid courses, being part of WCS team which design, develop and teach Train the Trainer type of courses.