Bioinformatics and Data Visualization in COVID-19 Genomic Surveillance Course (Level 1)

10 – 11 MARCH 2022

APPLICATION DEADLINE (for the practical session): 28 FEBRUARY 2022

Course description :

The success of COVID-19 control in Southeast Asia can be achieved only at a regional level due to the close socioeconomic cooperation, especially between countries with connecting land borders. High quality genomic surveillance data is important for tracking and eliminating virus clusters in Southeast Asia. This can be accomplished by building local bioinformatic capacities in the region with the focus on in-depth and up-to-date analyses to generate immediate impacts on public health control measures.

Under the support of Mahidol University, The Thailand Incentive and Convention Association (TICA), The Pandemic Prevention Institute and The Rockefeller Foundation, a 2-day on-line primer course will be held to introduce basic analysis tools needed for SARS-CoV-2 genomic data analysis and visualization. The focus will be on improving data quality for COVID-19 surveillance in Southeast Asia by instructors running real-time COVID-19 surveillance in Thailand which are supported by the high-performance computing facility at ThaiSC. The course will be divided into two parts namely, the lecture section opened to the public and the hand-on bioinformatic section limited to not-for-profit surveillance groups in Southeast Asia. We will take this opportunity to seek the feedback from the community on the open-access bioinformatic platform for SARS-CoV-2 genomic analyses using the High-Performance Computing facility from ThaiSC which will be made available to the surveillance team in Southeast Asia.


Elizabeth Batty, Ph.D.

Thanat Chookajorn, Ph.D.

Piroon Jenjaroenpun, Ph.D.

Theerarat Kochakarn, Ph.D., M.D.

Piyawut Srichaikul, Ph.D.

Manaschai Kunaseth, Ph.D.

(Mahidol-Oxford Research Unit)

(Mahidol University)

(Mahidol University)

(Molecular Infection Medicine Sweden)




Lecture via Zoom (open to the public; registration required).
Practical session via Zoom (limited to non-profit genomic surveillance contributors).
Every part will be in English.


DAY 1 (Lecture)/ 10 MARCH 2022

Session 1 :

Principles of SARS-CoV-2 genomic surveillance

This session will cover the basics of different sequencing technologies (including Illumina, Ion Torrent, and Oxford Nanopore) and some common approaches used to sequence SARS-CoV-2 using these platforms, such as amplicon sequencing, shotgun metagenomics, and targeted enrichment.

Session 2

Bioinformatics for SARS-CoV-2 sequencing

An introduction to bioinformatic analysis of SARS-CoV-2 data, focusing on amplicon sequencing data.

  • Introduction to raw data
  • Using pipelines to generate consensus sequence
  • Data QC
  • SARS-CoV-2 lineages, and assigning lineages to your strain
  • Best practices for SARS-CoV-2 metadata
  • Data upload to GISAID and INSDC

Session 3

SARS-CoV-2 Genetic Epidemiology

  • Phylogenetics and time trees
  • Running local Nextstrain builds for data visualization
  • Management of metadata for data visualization
  • Using USHeR and Nextclade for sample placement
  • Useful tools in data visualization and threat analyses

Session 4

Introduction to HPC and analysis platforms on NSTDA supercomputer center (ThaiSC)

DAY 2 (Practical session)/ 11 MARCH 2022

Guided session on:

  • One web-based/easy to use tools for SARS-CoV-2 analysis
  • One demonstration session on the ThaiSC pipeline
  • EPI2ME cloud-based platform
  • Downloading and using data from GISAID
  • Q&A session/personalized discussion of bioinformatic requirements