Institut Biologi Sistem

 Institute of Systems Biology

  • NGS Informatics: Processing high-throughput sequencing reads for beginners

    Date : 13 - 15 May 2025

    Venue : Hybrid (On-site / Online)

    Speaker : Ts. Dr. Nor Azlan Nor Muhammad

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 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)

Highlights

  • Galaxy Server

  • De Novo assembly, genome assembly

  • Genome, transcriptome, metagenome data

  • Trinity, Spades

  • BUSCO

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 and annotation.

  • 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

  • This workshop is open to local & international participants, from beginner to advanced researchers in molecular biology / omics.

Fees

Rate Per Person / Mode

On-site

Online

Individual

RM 900

USD 220

RM 400

USD 100

Group of 3

RM 750

USD 180

RM 300

USD 80

List of Speakers and Trainers

  • Ts. Dr. Nor Azlan 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 Ts. Dr. Nor Azlan can be expressed via his email, norazlannm@ukm.edu.my.

Programme

13th May 2025 (Tuesday)

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

14th May 2025 (Wednesday)

Time Activity Trainer
10.00 am Introduction to Day 2 Ts. Dr. Nor Azlan
10.15 am Lecture 3:  Transcriptomics based NGS analysis Ts. Dr. Nor Azlan
11.15 am Tea break -
11.30 am Practical 3 :   Raw reads pre-processing, quality check, reads statistics Ts. 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
Practical 5: Identification of protein sequences, sequence annotation, gene ontology assignment		 Ts. Dr. Nor Azlan
4.30 pm END OF DAY 2

15th May 2025 (Thursday)

Time Activity Trainer
10.00 am Introduction to Day 3 Ts. Dr. Nor Azlan
10.15 am Lecture 4:  Metagenomics based NGS analysis Ts. Dr. Nor Azlan
11.15 am Tea break -
11.30 am Practical 6: Raw-reads processing, ASV file generation, taxonomic identification Ts. Dr. Nor Azlan
12.30 pm Lunch break -
2.30 pm Practical 7: Metagenomics visualization, krona tools
Practical 8: Genome assembly, gene prediction		 Ts. Dr. Nor Azlan
4.30 pm END OF WORKSHOP

Centre of Omics Data Analysis (CODA)

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