Viral Bioinformatics and Genomics (Ho Chi Minh City, Vietnam)

Viral diseases including zoonotic infections are a major public health burden across the world, especially in low and middle-income countries (LMIC) in Asia, Africa and Latin America where diagnosis and surveillance of viral diseases are challenging. In Asia, influenza, dengue, hand, foot and mouth disease, chikungunya and viral hepatitis are some of the viral diseases that cause hundreds of thousands of deaths each year. Apart from health risks, emerging viral infections and outbreaks also pose an economic burden globally.

Advances in research technologies are enabling access to improved detection, surveillance and management of viral diseases. In the recent years, next generation sequencing (NGS) technologies has played an important role in the identification and classification of viruses, the detection of drug resistance mutation and the treatment and surveillance of viral diseases. Early identification of a virus and rapid analysis of its genome will aid towards better treatment and help in controlling the disease spread.

This exciting new course will be held in collaboration with the Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam and will provide participants with a working knowledge of viral genome sequence analysis and interpretation of genomics data generated from large-scale sequencing.

Topics will include the use of the command line to perform analysis of viral NGS, quality control of genomics data, reference and de-novo assemblies, pathogen detection from metagenomics data, annotation transfer from a reference genome and building phylogenetic trees.

Target audience
The course is free to attend and open to applicants based in Asia and Autralasia engaged in relevant research/clinical activities. The course is aimed at applicants at various levels, including Senior Research Assistants, PhD students, Postdoctoral Researchers, Laboratory Scientists, Clinicians and Clinical Scientists.

The hands-on programme will cover several aspects of analysis of next generation sequencing data from viral genomes, including lectures, practical computational sessions, case studies and seminars, covering the following:

• Introduction to Linux/Unix
• NGS file formats
• NGS data quality check and cleaning
• Reference assembly
• Assembly statistics and visualisation
• Consensus and variant calling
• Pathogen sequence detection using sequence classifiers
• De novo assembly
• BLAST assignment of metagenomics contigs
• De novo contig consolidation and gap filling
• Annotation / sequence submission
• Multiple sequence alignment
• Introduction to phylogenetics methods
• BASH scripting

Seminars
The programme will also include seminars covering the following topics:

• Global health and viral diseases
• Overview of current sequencing technologies and applications
• Evolution of pathogens
• Resistance associated mutations

Case studies

• Zika emergence
• Metagenomics
• Hand, Foot and Mouth Disease
• Ebola (reference assembly)
• Dengue (de novo assembly)

Learning Outcomes
After completing this course, participants should be able to:

• Apply Unix/Linux command-line and write basic shell scripts for automating bioinformatics tasks
• Recognize the different file formats related to genome sequencing data
• Select an appropriate strategy for Quality Control of NGS data
• Construct reference assemblies using different software (e.g. BWA, Bowtie, Novoalign, Tanoti).
• Evaluate genome assemblies using statistics and visualisations
• Use multiple de-novo assemblers for viral genome reconstruction (e.g. SPAdes, ABYSS, IDBA-UD)
• Use metagenomics tools as such as Taxonomer and CLARK to detect and identify viral pathogens
• Select appropriate software tools to call variants from a reference assembly.
• Compute multiple sequence alignment
• Construct phylogenetic trees to understand viral evolution
• Build their own pipeline for analysis, interpretation and identification of viral pathogens

Course instructors

Prerequisites

The course is open to applicants based in Asia and Autralasia engaged in relevant research/clinical activities. The course is aimed at applicants at various levels , including Senior Research Assistants, PhD students, Postdoctoral Researchers, Laboratory Scientists, Clinicians and Clinical Scientists.

Please note that to fully benefit from the course participants will require a high level of computer competency, ideally with some existing experience in analysing sequence data. Basic knowledge of the UNIX/Linux operating system and use of command line is also required. There are numerous online introductory tutorials to the UNIX/Linux operating system and commad line, including:
http://www.ee.surrey.ac.uk/Teaching/Unix
http://swcarpentry.github.io/shell-novice/

The course will be taught in English.

How to Apply
Please complete the online application form. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

Cost

The course is subsidised by Wellcome Genome Campus Advanced Courses and Scientific Conferences and is free to attend for non-commercial applicants.
Please contact us for the commercial fee.

Bursaries

A limited number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance. The maximum award for travel (economy class) will be £750. If you would like to apply for a bursary, please complete the bursary section of the online application form.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.