NEW Computational

SARS-CoV-2- Bioinformatics for Beginners 

31 October–2 December 2022

Distributed Classrooms across Asia, Latin America, and Africa

SARS-CoV-2 Bioinformatics for Beginners - Participant applications open


SARS-CoV-2 Bioinformatics for Beginners – Participant Applications Closed

Please visit our Host Page for details. Registration is now closed.

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. Bioinformatics skills are fundamental in management and assessment of viral sequences. This course will introduce you to processing data programmatically, the data formats used in viral sequencing, how to determine the variant lineage (Delta, Omicron etc.), and how to share data so that others around the world can benefit. These skills are the building blocks for scaling up analysis to pandemic response levels. 

Participants applications are open for classrooms in Latin America and the Caribbean, Africa, and Asia. Participants MUST apply to the geographically closest classroom.

Time commitment: Contact sessions will run twice a week,  lasting for 4 hours per session. It will run between the 31st of October – 2nd of December 2022. There will be sessions in two time zones. Note, each session for Oceania and Asia; and Latin America and Africa; will run in the same block of time, but with regional time differences. 

Group Time Asia Time Oceania Time Africa Time Latin America
Time Zone UTC +7 ICT UTC +13 NZDT UTC +2 CAT UTC -3 ARG
Day of Running Tuesdays Thursdays Tuesdays Thursdays Tuesdays Thursdays Tuesdays Thursdays
Time of Running

In Region

12h00-16h00 18h00-22h00 14h00-18h00 9h00 -13h00 

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. It does not require bioinformatics skills as a prerequisite.

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

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


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

Course instructors

Course Instructors 

Leigh Jackson
COG-Train Scientific Lead

How to register

Participant Applications closed

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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