Microbial Genome & Microbiome Analysis Course Content Timeline
MODULE 1: MICROBIAL GENOME
May 19, 2024
Lecture 1
Introduction to the course structure and objectives
Ubuntu and Basic Linux Commands Part 1
May 23, 2024
Lecture 2
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
Bash Cheat Sheet (Download to your device to view)
May 26, 2024
Lecture 3
Homology Search with BLAST (Part 2): Pairwise Alignment
Bash Script and AWK
Homework Answer
May 30, 2024
Lecture 4
Primer and Probe Design
Wrap-up Linux Command Line
June 2, 2024
Lecture 5
Multiple Alignment
Phylogenetic Trees
Basic R1: Data types, Basic calculations, Data structure, Basic Functions (For loop, If ...else, While loop)
Code editing with VScode: Homework
June 6, 2024
Lecture 6
Pairwise and Multiple genome alignment with Mauve
PDF PPTX YOUTUBE
Basic plot in R2
PPTX Question Answer YOUTUBE
Introduction to GitHub
Test answer
June 9, 2024
Lecture 7
Sanger Sequencing method
Introduction of next-generation sequencing (NGS)
Lecture ppt
Pacbio
AVITI
SISC
ILLUMINA
MGI
Slides
June 13, 2024
Lecture 8
Gene and Genome Annotation
Basic statistics in R3
Lecture 9
I. Introduction of Whole genome sequencing analysis for Microbes
II. Microbial WGS upstream analysis
1. QC and Trimming
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
June 20, 2024
Lecture 10
Denovo assembly for WGS of Microbes
Annotation of WGS and Pathway Analysis
June 23, 2024
Lecture 11
Serotyping, genotyping and phenotyping for Microbes
June 27, 2024
Lecture 12
Review Module 1: Microbial Genome Analysis
Introduction of Metagenomics and Microbiome (Module 2)
MODULE 2: MICROBIOME ANALYSIS
June 30,2024
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
July 4,2024
Lecture 14 Introduction to R for Microbiome Data (part 2)
1 Introduction to R for Microbiome Data (part 2)
- Specifically Designed R Packages for Microbiome Data: Phyloseq
- [PDF] [DATA] [TUTORIAL]
- [HOMEWORK] [ANSWER]
2 Experimental Design for Microbiome studies (16S, shotgun and WGS)
- [PDF] -[DATA] -[TUTORIAL]
- [HOMEWORK] -[ANSWER]
References
Books
Some recommended courses for Bash, Scripts, Awk