Microbial Genome & Microbiome Analysis Course Content Timeline
MODULE 1: MICROBIAL GENOME
Introduction to the course structure and objectives
Ubuntu and Basic Linux Commands Part 1
Nucleotide sequence database: DNA and RNA
Homology Search with BLAST (Part 1)
Basic Linux Commands Part 2: Search and Filter, Input/Output Redirection
Basic Linux Commands Part 2: Download, File permission, Compress and Decompress
Introduction to Bash Scripting
Bash Cheat Sheet (Download to your device to view)
Homology Search with BLAST (Part 2): Pairwise Alignment
Wrap-up Linux Command Line
Q&A
Basic R1: Data types, Basic calculations, Data structure, Basic Functions (For loop, If ...else, While loop)
Code editing with VScode: Homework
Pairwise and Multiple genome alignment with Mauve
PDF PPTX YOUTUBE
PPTX Question Answer YOUTUBE
Introduction of next-generation sequencing (NGS)
Gene and Genome Annotation
I. Introduction of Whole genome sequencing analysis for Microbes
II. Microbial WGS upstream analysis
2. Alignment/Mapping to the reference genome, QC and visualization of BAM
III. Microbial WGS downstream analysis
1. Calling variants and visualization of variants (VCF)
2. Building and visualization of Phylogenetic Trees
Denovo assembly for WGS of Microbes
Annotation of WGS and Pathway Analysis
Serotyping, genotyping and phenotyping for Microbes
Section 1: Serotyping, phenotyping
Section 2: Genotype and molecular subtyping
Section 3: MLST analysis for microbes
Section 4: How to use pubMLST database + CoreGenome MLST practice
Review Module 1: Microbial Genome Analysis
Introduction of Metagenomics and Microbiome (Module 2)
MODULE 2: MICROBIOME ANALYSIS
Lecture 13 Introduction to R for Microbiome Data (part 1)
1. Introduction Some Useful R Functions + Some Useful R Packages for Microbiome Data: Readr, Ggpubr, Tidyverse
2. Introduction to ggplot2 and basic plot
3. R package ggplot2 in R4 for microbiome analysis + Practice
Lecture 14 Introduction to R for Microbiome Data (part 2)
1 Introduction to R for Microbiome Data (part 2)
2 Experimental Design for Microbiome studies (16S, shotgun and WGS)
2 Challenging when working with microbiome samples
1. Bioinformatic Analysis of Microbiome Data & 2. Microbiome Data Structure
3. Introduction to QIIME 2
4. Basic Data Processing in QIIME 2
1. Building feature table and feature representative sequences from raw reads
Assigning Taxonomy & Building Phylogenetic Tree
1. Clustering Sequences into OTUs
2. OTU Methods in Numerical Taxonomy
1. Alpha diversity & Visualization
2. Beta diversity & Visualization
Differential abundance analysis (DAA)
Library prep and multiplexing for 16S and shotgun metagenomics
October 6, 2024 (20h-22h30)
- Main content: PDF PPTX YOUTUBE
- Review old lecture MGMA
- Introduction new platform
October 13, 2024 (20h-22h30)
Shotgun Metagenomics Workflow using Oxford Nanopore Platform
October 20, 2024 (20h-22h30)
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Microbiome 16S 
YOUTUBE
October 27, 2024 (19h-22h30)
Some recommended courses for Bash, Scripts, Awk
