SARS-CoV-2 Bioinformatics for Beginners 

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

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. 

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

Participant Applications closed

Participant applications are now closed. Please be on the lookout for an email from the Host or Core-Team at the end of September.

If you encounter any errors, please use the “Email the Organiser” button in the side bar and include the name of the class to which you are applying in the email.

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.

The course is subsidised by COG-Train and is free to attend.