NEW Computational

SARS-CoV-2- Bioinformatics for Beginners 

31 October–02 December 2022

Distributed Classrooms across Asia, Latin America, and Africa

SARS-CoV-2 Bioinformatics for Beginners - Expression of interest for Hosts


SARS-CoV-2 Bioinformatics for Beginners – Expression of interest for Hosts

SARS-CoV-2 variant lineage identification is key to pandemic tracking and enabling public health response. This course is an introduction to bioinformatics by applying skills used in SARS-CoV-2 genomic data analysis. This will be a distributed classrooms style course run across Africa; Latin America and the Caribbean; and Asia. This model was developed by H3ABioNet, see this publication for more info. 

Please see the video below for an explanation on the Distributed Classrooms model:


We are seeking hosts for classrooms in Latin America and the Caribbean, Africa, and Asia. If you would like to assist local scientists who are interested in learning bioinformatics skills which can be applied to analysis of SARS-CoV-2, please fill our expression of interest form using the APPLY link above. Spaces are limited so be sure to apply soon.

Time commitment: Contact sessions will run twice a week,  lasting for 4 hours per session. It is to run over the weeks of November 2022, exact dates will be confirmed after interest captured.

Target audience: The course is aimed at postgraduate scientists, postdoctoral scientists,  junior faculty members or clinicians/healthcare professionals based in the regions across Africa, Asia, and Latin America & the Caribbean.


The programme will cover the following core topics:

  • Intro to Python Notebooks
  • Intro to Unix/Linux & running commands
  • Introduction to NGS Technologies employed in SARS-CoV-2 sequencing
  • Data quality control
  • Workflows for sequencing analysis
  • Pangolin for lineage identification
  • Exploring genomics data in a global context

Learning Outcomes:

SARS-CoV-2 Variant lineage assignment

  • Apply command line tools for sequence data quality control
  • List file formats commonly used in SARS-CoV-2 sequencing
  • Use Pangolin to create viral lineages from sets of existing data
  • List key metadata that must be included when uploading sequences to online repositories
  • Describe broad principles in translation of analysis outputs to outbreak/epi/pandemic response

How to apply

Host Applications
To apply to host a classroom for this, please use the Apply button above. We are collecting responses of interest until 7 July 2022.

Host prerequisites:

Classroom Hosts help facilitate the course. 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. Virology background is beneficial but most genomics disciplines for bioinformatics can be readily suitable for hosting.

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 like Moodle. It is possible to be both a Host and Instructor for this course.

General prerequisites:

The course will be making use of Google Colaboratory – which is free to use, but requires a Google Account to use. Google accounts are free to make.

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