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Course Informatics Guide
Learn to analyse next-generation sequence data to address a wide range of biological questions
High-throughput sequencing has gained widespread adoption as an essential experimental assay for biological research. Analysing high-throughput sequencing data involves an array of different bioinformatics tools and techniques. Therefore, it is important for experimental scientists to have the bioinformatics skills required to effectively assess and analyse data produced by next generation sequencing.
This course aims to provide a hands-on introduction to bioinformatics for next generation sequencing and to equip participants with the essential informatics skills and knowledge required to begin analysing next generation sequencing data and carry out some of the most common types of analysis.
The course is aimed at researchers or clinicians/ healthcare professionals actively engaged in or soon to commence work involving next generation sequencing data analysis.
What will you be able to do?
After attending this course, participants will be able to:
- Use the Linux command-line and advanced Linux commands for automating bioinformatics tasks
- Evaluate the results of QC analysis of high throughput sequencing data
- Understand the algorithmic concepts behind short read alignment and variant calling, and have practical experience of using relevant software
- Analyse RNA-Seq data to measure abundance
- Develop bioinformatics workflows
The hands-on programme will cover several aspects of next generation sequencing data analysis, including lectures, discussions and practical computational sessions covering the following:
- Introduction to NGS technologies
- Introduction to the Linux command line
- Linux for bioinformatics
- NGS data formats and tools
- Sequence alignment+QC
- SNP/indel theory and practical
- Structural variation theory and practical
- RNA-seq analysis
- Sequencing data visualisation with the Integrated Genomics Viewer
- Genome assembly
- Bioinformatics workflow essentials
- Participant projects and presentations (final day)
Please note: The practical sessions will be taught exclusively through Linux. Therefore, participants are required to have some familiarity with the Linux operating system. This will be essential for participants to fully benefit from the course. With this in mind, we will provide comprehensive pre-course material via our learning management system in the weeks immediately before the course. Additionally, there are numerous online introductory tutorials to the Linux operating system and command line, including:
The course should not be considered a complete education in the theoretical and mathematical foundations of the topics.
Scientific Organising Committee
- Qasim Ayub, Monash University, Malaysia
- Jacqueline Keane, Wellcome Sanger Institute, UK
- Thomas Keane, European Bioinfromatics Institute, UK
Course Instructors
- Arporn (Koi) Wangwiwatsin, Khon Kaen University, Thailand
- Jin Li, Oujiang Laboratory, China
- Jingtao Lilue, Oujiang Laboratory, China
- Adaikalavan Ramasamy, Genome Institute of Singapore
- Aswini Leela Loganathan, Monash University, Malaysia
- Vivek Iyer, Wellcome Sanger Institute, UK
- Wee Wei Yee (Gavin), Monash University, Malaysia
- Gokce Oguz, Genome Institute of Singapore
- Hong Leong Cheah, Monash University, Malaysia
- Onnapa Kongphan, Khon Kaen University, Thailand
Wellcome Connecting Science Team
- Alice Matimba, Head of Training and Global Capacity
- Michelle Bishop, Associate Director
- Isabela Malta, Assistant Global Training Manager
- Karon Chappell, Event Organiser
- Martin Asltett, Informatics Manager
- Vaishnavi Vikas Gangadhar, Informatics Technical Officer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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