Dr Chua Eng Wee, Universiti Kebangsaan Malaysia
Recent years have seen a surge in the use of next-generation sequencing (NGS) for examining the genetic basis of complex diseases and drug response. However, analysing NGS data can be challenging, as many of the software tools typically require the users to have a basic grasp of command-line (or Unix) operations and programming languages. This one-day workshop is intended for those who are new to NGS and looking for a painless way to analyse NGS data in a non-Unix environment. As such, this workshop is suitable for students and researchers who are involved in pharmacogenomics, cancer genomics, drug discovery, biomedicine, life science, computational biology, or those who wish to work at centres for genomic or translational medicine. Our main objective is to equip the participants with the skills necessary for translating genomic data into meaningful functional annotations. Throughout the workshop, the participants will be taught how to run NGS analyses on a user-friendly web-based application, Galaxy, that is designed for scientists with little proficiency in bioinformatics. The workshop will cover the following:
- Understanding the mechanisms of well-known NGS platforms
- Utility and limitations of NGS in pinpointing genotype-phenotype associations
- Basic structures of the data files in NGS including BED, BAM, SAM, and VCF
- Introduction to the basic workflow of analysing NGS data, including checking data quality, sequence alignment, variant calling, and selecting high-confidence variants and gauging their functional relevance
- Hands-on sessions using real NGS data sets and a web-based application, Galaxy
Participants must bring their own laptop for the hands-on sessions.