10 – 11 MARCH 2022
APPLICATION DEADLINE (for the practical session): 28 FEBRUARY 2022
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)
(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.
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.
Bioinformatics for SARS-CoV-2 sequencing
An introduction to bioinformatic analysis of SARS-CoV-2 data, focusing on amplicon sequencing data.
SARS-CoV-2 Genetic Epidemiology
Introduction to HPC and analysis platforms on NSTDA supercomputer center (ThaiSC)
Guided session on: