Tentative Program

1. Introduction to microbiome research

• What is the Microbiome? Review of relevant terms (microbial communities, microbiome, Operational Taxonomic Unit (OTU), species, metagenome, marker genes, metatranscriptomics)
• What is the best way to collect a sample and design a study for microbiome analysis?
• How should I analyze my data with various bioinformatics tools?
• Amplicon (16S rRNA and ITS) sequencing vs. shotgun sequencing
• Starting points in metagenomic data analysis: sequence files, resources, reference databases

2. Best-practice workflow for microbiome data analysis

• Amplicon analysis

  What is 16S and ITS? Why is it useful? What are its limitations?
  16S and ITS data processing
  Clustering and Classification - OTUs vs. ASVs ; Taxonomy
  Diversity (and co-occurrence?)
  Statistics and machine learning related to microbiome studies
  Brief intro on gene annotations and different granularity
  Inferring function from taxa from PICRUSt2

PROGRAMME

Tuesday, December 13rd, 2022
7:30 – 8: 30	Course registration and informal introductions	ICISE, Quy Nhon City
8:30 – 9:00	Welcome address Introduction of trainers and participants, group photo	Dr. Tran Thanh Son, ICISE, Quy Nhon City Assoc.Prof.Dr. Nguyen Bao Quoc, Nong Lam University
9:00 – 9:15	Introduction of course work and practical	Assoc.Prof.Dr. Nguyen Bao Quoc, Nong Lam University, HCMC
9.15 – 10.00	Lecture 1: Introduction to Metagenomics and Applications in Agriculture	Prof. Dr. Truong Nam Hai Institute of Biotechnology, Vietnam Academy of Science and Technology
10:00 – 10.20	Coffee break/ Tea break
10.20 – 11.05	Lecture 2: 16S and ITS metagenomics library preparation	Dr. Nguyen Thuy Vy University of Natural Sciences, Vietnam National University, HCMC
11:05 – 11:50	Lecture 3: Functional Prediction from 16S/ITS data, Shotgun metagenomics	Dr. Tran Thi Thanh Tam University of Science and Technology Hanoi, VAST
11:50 – 13:30	Lunch break	ICISE
13:30 -14:00	Overview about 16S analysis workflow	Dr. Do Hoang Dang Khoa Nguyen Tat Thanh University, HCMC Assistant staff: Dr. Tran Thi Thanh Tam University of Science and Technology of Hanoi, VAST MSc. Tran Hong Quan LOBI Vietnam Ltd
14:00 – 15:00	Hands-on 16S analysis workflow
15:00 -15:15	Coffee break/ Tea break
15:15 – 16:15	Hands-on 16S analysis workflow (cont’)
16:15-17:30	Hands-on 16S analysis workflow Wrap up and feedback (Q&A)
17:30	Bus to the hotel
Wednesday, 14th December, 2022
8:30 – 9:00	Overview about ITS analysis workflow, Galaxy Platform	Dr. Tran Thi Thanh Tam University of Science and Technology of Hanoi, VAST Assistant staff: Dr. Do Hoang Dang Khoa Nguyen Tat Thanh University, HCMC MSc. Tran Hong Quan LOBI Vietnam Ltd Dr. Vu Minh Thiet, Nguyen Tat Thanh University, HCMC
9:00 – 10:00	Hands-on ITS analysis workflow
10:00 – 10:15	Coffee break/ Tea break
10:15-11:30	Hands-on ITS analysis workflow Wrap up and feedback (Q&A)
11:30 – 13:30	Lunch break	ICESE, Quy Nhon City
13:30 – 14:30	Statistical analysis and data visualization for metagenomics	Dr. Vu Minh Thiet Nguyen Tat Thanh University Assistant staff: Dr. Do Hoang Dang Khoa Nguyen Tat Thanh University, HCMC Dr. Tran Thi Thanh Tam University of Science and Technology of Hanoi, VAST MSc. Tran Hong Quan LOBI Vietnam Ltd
14:30 – 14:45	Coffee break/ Tea break
14:45 – 16:00	Statistical analysis and data visualization for metagenomics (cont’)
16:00 – 16:30	Nanopore based point-of-care sequencing: when, what and how to decide and implement	Prof. Dr. Rajesh Pandey CSIR – Institute of Genomic and Integrative Biology, New Dehli, India
16:30 – 17:00	Nanopore sequencing and veterinary application	Mrs. Pham Thi Thanh Tam BCE Company Ltd.
17:00 – 17:30	Closing and certificate ceremony
18:00 – 20:00	GALA dinner
20:00	Bus to the hotel
Thursday and Friday, 15-16th December, 2022
All day	International workshop on Molecular Diagnostics in Microbiology and Diseases (MDMD2022)