Workshop Outline

This workshop focuses on practical NGS informatics analysis that applies to genomics, transcriptomics and metagenomics data. This workshop is aimed at biologist who wants to do their own bioinformatics on next-generation sequencing data from genomics, transcriptomics or metagenomics projects. Workshop will focus on raw reads from the Illumina sequencing platforms.

At the end of this 5 days online workshop, participants will be able to:

  • Search and download publicly available NGS raw reads for new projects/analysis
  • Select relevant tools and build your own NGS analysis pipeline
  • Do you own pre-processing of raw reads, De Novo assembly, assembly quality check, mapping, functional annotation, differential genes analysis and visualisation for publication
  • Identify the tools which are optimized for the different omics (genomics/transcriptomics/metagenomics)
  • Use online resources for NGS data analysis
  • Do basic R-programming for visualization

Highlights

  • Galaxy Server
  • De Novo assembly
  • BUSCO
  • Trinotate
  • Online Workflow

Who should attend

  • You're a researcher, academician, or student interested in processing your own NGS data/reads
  • You're interested in advanced skills in NGS informatics such as reads pre-processing, De Novo assembly, annotation and visualization using R
  • You want user-friendly platforms for the analysis of NGS raw reads
  • You wish to analyze publicly available NGS raw reads obtained from the NCBI SRA database
  • You wish to analyze the NGS data hands-on, but do not know how to start
  • You want to learn the basics of R programming for visualization
  • This workshop is open to local & international participants, from beginner to advanced researchers in molecular biology / omics.

List of Speakers and Trainers

  • Dr. Nor Azlan currently is the Head of Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia. He joined INBIOSIS as a research fellow in October 2015. His expertise is in bioinformatics and computational systems biology. His research focus is on the application of omics technologies to unravel new genes and pathways for the development of precision biotechnology. His current main organisms of interests are insect pests, including bagworm (Metisa plana), red palm weevil (Rhynchophorus ferrugineus) and cocoa pod borer (Conopomorpha cramerella). The long-term aim is to analyse the genome, transcriptome, proteome and metabolome of these species and use omics integration techniques to develop new methods of controlling them. He is collaborating with Felda Global Ventures R&D for the bagworm and red palm weevil work.

  • His other works involve biological database development and Next Generation Sequencing bioinformatics. Two of the databases that he has helped develop are PCOSBase (pcosbase.org) and SuCComBase (plant-scc.org). His other NGS projects are on the metagenomics and metatranscriptomics of palm oil mill effluent (POME), Rafflesia and Tetrastigma transcriptomics, as well as Ganoderma boninense genomics. He is also involved in the analysis of the bacterial Type IX Secretion System, trying to understand its mechanisms via advanced sequence analysis.

  • He is also the treasurer of the Malaysian Society of Bioinformatics and Computational Biology (masbic.org) for the year 2021-2022. At the society, bioinformaticians and computational biology experts from all over Malaysia are gathered. The society tries to empower the bioinformatics community in Malaysia via activities such as webinars, workshops, conferences, and consultations. Expressions of interest for research collaboration and activity with Dr. Nor Azlan can be expressed via his email, norazlannm@ukm.edu.my.

  • Dr. Norfarhan binti Mohd Assa’ad is a senior lecturer at the Department of Applied Physics, Faculty of Science and Technology, UKM. She earned her doctorate degree from ETH Zurich, Switzerland in 2018 where she started grasp the knowledge and structure of R. The R language is intensely used by ETH students and was introduced since their early years in the campus, leaving her no option but to integrate the programming language as part of her research tools. Her research interest is mainly on the evolutionary genomics, spanning a wide range of organisms with different biological question using bioinformatics tools.

  • Please feel free to contact Dr. Norfarhan Mohd Assa'ad (n_farhan@ukm.edu.my) for research and industrial projects collaboration.

Programme

9th August 2022 (Monday)

Time Activity Trainer
9.30 am Registration -
10.00 am Opening ceremony and introduction -
10.15 am Lecture 1 :  Introduction to NGS technologies Dr. Nor Azlan
11.15 am Tea break -
11.30 am Practical 1 :   Galaxy Europe Hands-on, account creation, introduction to Galaxy Europe features Dr. Nor Azlan
12.30 pm Lunch break -
2.30 pm Practical 2 :  Database searching, downloading raw reads for NGS analysis, importing data to Galaxy Europe Dr. Nor Azlan
4.30 pm END OF DAY 1

10th August 2022 (Tuesday)

Time Activity Trainer
10.00 am Introduction to Day 2 Dr. Nor Azlan
10.15 am Lecture 2 :  NGS analysis pipelines and tools Dr. Nor Azlan
11.15 am Tea break -
11.30 am Practical 3 :   Raw reads pre-processing, quality check, reads statistics Dr. Nor Azlan
12.30 pm Lunch break -
2.30 pm Practical 4 :  De Novo RNA-seq assembly, assembly quality check, differential expressed gene analysis Dr. Nor Azlan
4.30 pm END OF DAY 2

11th August 2022 (Wednesday)

Time Activity Trainer
10.00 am Introduction to Day 3 Dr. Nor Azlan
10.15 am Practical 5 :  Genome assembly, assembly quality check, gene prediction Dr. Nor Azlan
11.15 am Tea break -
11.30 am Practical 5 : Continued Dr. Nor Azlan
12.30 pm Lunch break -
2.30 pm Practical 6 :  Metagenome assembly, taxonomy analysis, gene prediction Dr. Nor Azlan
4.30 pm END OF DAY 3

12th August 2022 (Thursday)

Time Activity Trainer
10.00 am Introduction to Day 4 Dr. Norfarhan
10.15 am Lecture 3 :  Sequence annotation and comparative genomics Dr. Norfarhan
11.15 am Tea break -
11.30 am Practical 7 : Trinotate, NCBI-Blast, HMMER, SignalP, Gene Ontology Dr. Norfarhan
12.30 pm Lunch break -
2.30 pm Practical 8 :  Comparative genomics, sequence comparison Dr. Norfarhan
4.30 pm END OF DAY 4

13th August 2022 (Friday)

Time Activity Trainer
10.00 am Introduction to Day 5 Dr. Norfarhan
10.15 am Lecture 4 :  Introduction to R language Dr. Norfarhan
11.15 am Tea break -
11.30 am Practical 9 : Charts, graphs Dr. Norfarhan
12.30 pm Lunch break -
2.30 pm Practical 10 :  Statistics Dr. Norfarhan
5.00 pm END OF DAY 5

Register now or contact us for more details