Microbial Genome & Microbiome Analysis Course Content Timeline

MODULE 1: MICROBIAL GENOME

May 19, 2024

Lecture 1

Introduction to the course structure and objectives

• PDF  PPTX   YOUTUBE
• Ways to get the Terminal

Ubuntu and Basic Linux Commands Part 1

• I. Introduction: Ubuntu, File Systems, Some Terms:
• PDF  PPTX   YOUTUBE
• II. Some commands work with files and directories:
• PDF  PPTX   YOUTUBE
• Homework for Basic Linux Commands Part 1  Homework answers
• Question and Answer  Q&A

May 23, 2024

Lecture 2

Nucleotide sequence database: DNA and RNA

• PDF   YOUTUBE

Homework:

• PDF   PPTX

Homology Search with BLAST (Part 1)

• PDF  PPTX   YOUTUBE

Basic Linux Commands Part 2: Search and Filter, Input/Output Redirection

• PDF   PPTX   YOUTUBE

Basic Linux Commands Part 2: Download, File permission, Compress and Decompress

• PDF  PPTX YOUTUBE
• Materials used in Slide
• Homework for Basic Linux Commands Part 2  Homework answers

Introduction to Bash Scripting

• PDF  YOUTUBE  Scripts-material
• Homework  Answer  
• Q&A  

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

• PPTX   PDF   YOUTUBE

Bash Script and AWK

• PDF YOUTUBE
• Homework  Material Script  

Homework Answer

• Homework_Answer  Awk Cheat sheet   Q&A

May 30, 2024

Lecture 4

Primer and Probe Design

• PDF   YOUTUBE

Wrap-up Linux Command Line

• PDF-part1   PDF-part2  YOUTUBE

  Q&A

June 2, 2024

Lecture 5

Multiple Alignment

• PDF  PPTX  YOUTUBE

Phylogenetic Trees

• PDF  PPTX  YOUTUBE

Basic R1: Data types, Basic calculations, Data structure, Basic Functions (For loop, If ...else, While loop)

• Homework  Markdown   YOUTUBE

Code editing with VScode: Homework

• PPTX   YOUTUBE

Q&A

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

• PDF  PPTX   YOUTUBE

Test answer

• Answer
• YOUTUBE

June 9, 2024

Lecture 7

Sanger Sequencing method

• YOUTUBE

Introduction of next-generation sequencing (NGS)

• PDF  PPTX   YOUTUBE

Lecture ppt

Pacbio

• PDF   YOUTUBE

AVITI

• PDF   YOUTUBE

SISC

• PDF   YOUTUBE

ILLUMINA

• PDF   YOUTUBE

MGI

• PDF   YOUTUBE

Q&A

Slides

• PacBio  MGI  AVITI  GeneMind  Illumina SISC

June 13, 2024

Lecture 8

Gene and Genome Annotation

• PDF  PPTX   YOUTUBE

Basic statistics in R3

• PDF   Data CSV  TUTORIAL   R code   YOUTUBE.
• Homework   Answer

June 16, 2024

Lecture 9

I. Introduction of Whole genome sequencing analysis for Microbes

• PDF   YOUTUBE

II. Microbial WGS upstream analysis

1. QC and Trimming

• PDF  QC  Trimming   YOUTUBE

2. Alignment/Mapping to the reference genome, QC and visualization of BAM

• PDF  Paper  Alignment   YOUTUBE

III. Microbial WGS downstream analysis

1. Calling variants and visualization of variants (VCF)

• TUTORIAL   YOUTUBE

2. Building and visualization of Phylogenetic Trees

• PDF   TUTORIAL   YOUTUBE

Q&A

June 20, 2024

Lecture 10

Denovo assembly for WGS of Microbes

• PDF   TUTORIAL   YOUTUBE

Annotation of WGS and Pathway Analysis

• PDF   Materials   YOUTUBE

Q&A

June 23, 2024

Lecture 11

Serotyping, genotyping and phenotyping for Microbes

• PDF for all sections

Section 1: Serotyping, phenotyping

• PDF YOUTUBE

Section 2: Genotype and molecular subtyping

• PDF YOUTUBE

Section 3: MLST analysis for microbes

• PDF YOUTUBE

Section 4: How to use pubMLST database + CoreGenome MLST practice

• PDF YOUTUBE  TUTORIAL

Q&A-YOUTUBE

June 27, 2024

Lecture 12

Review Module 1: Microbial Genome Analysis

• Artical_Viruses_PDF   Artical_Streptococcus pneumoniae_PDF   YOUTUBE

Introduction of Metagenomics and Microbiome (Module 2)

• PDF   PPTX   YOUTUBE

Q&A

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

• PDF   CHEAT SHEET   YOUTUBE

2. Introduction to ggplot2 and basic plot

• PPTX   YOUTUBE

3. R package ggplot2 in R4 for microbiome analysis + Practice

• PDF  DATA_TUTORIAL_R  TUTORIAL_HTML   YOUTUBE
• HOMEWORK_ANSWER

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_R  TUTORIAL_HTML   YOUTUBE

2 Experimental Design for Microbiome studies (16S, shotgun and WGS)

• PDF  YOUTUBE

Q&A

July 7,2024

Lecture 15

1 Wrap-up R5

• PDF   YOUTUBE

2 Challenging when working with microbiome samples

• PDF   PPTX   YOUTUBE

Q&A

July 11, 2024

Lecture 16

1. Bioinformatic Analysis of Microbiome Data & 2. Microbiome Data Structure

• PPTX   YOUTUBE

3. Introduction to QIIME 2

• PDF   YOUTUBE

4. Basic Data Processing in QIIME 2

• PDF   YOUTUBE

Q&A

July 14, 2024

Lecture 17

1. Building feature table and feature representative sequences from raw reads

• PDF   YOUTUBE

2. Practice

• PDF   TUTORIAL   YOUTUBE-1   Sample   Exercise   YOUTUBE-2

Q&A

July 18, 2024

Lecture 18

Assigning Taxonomy & Building Phylogenetic Tree

• PDF   YOUTUBE-1   YOUTUBE-2

Q&A

July 21, 2024

Lecture 19

1. Clustering Sequences into OTUs

• PDF   YOUTUBE

2. OTU Methods in Numerical Taxonomy

• PDF   YOUTUBE
• TUTORIAL

Q&A

July 25, 2024

Lecture 20

1. Alpha diversity & Visualization

• PDF  
• TUTORIAL
• YOUTUBE

2. Beta diversity & Visualization

• PDF   YOUTUBE

Q&A

July 28, 2024

Lecture 21

Differential abundance analysis (DAA)

• PDF  END TERM PROJECTS
• Practice with DESeq2:  Tutorials and Rscript(download and view with browser)  .Rmd file  raw count data  metadata  YOUTUBE
• Practice with ANCOM BC2:  Rscript  YOUTUBE
• Project list

August 1, 2024

Lecture 22

Library prep and multiplexing for 16S and shotgun metagenomics

• PDF  
• Extract and test quality of genomic DNA, Genomic DNA fragmentation
• Repair DNA the end of DNA fragments, Add DNA adapter, Collect target fragments,...
• Bind the sequencing libraries to sequencing chips, Sequencing

Q&A

August 4, 2024

Lecture 23

Shotgun metagenomics

• PDF   YOUTUBE
• TUTORIAL   YOUTUBE

Q&A

August 8, 2024

Lecture 24

Microbiome Application:

• Application in Environment & Aquaculture:  PPTX   YOUTUBE
• Application in Agriculture & Industry:  PPTX   YOUTUBE
• Applications in health and clinic:  PPTX   YOUTUBE
• DNA RNA extraction and NGS:  PDF   YOUTUBE

Q&A

MODULE 3: LONG READ MICROBIOME Timeline Project for MODULE 3

October 6, 2024 (20h-22h30)

Lecture 25

Overview of the course:

• Main content: PDF   PPTX   YOUTUBE
• Review old lecture MGMA
• Introduction new platform

16S full-length ONT

• 16S full-length ONT: PDF   YOUTUBE
• 16S full-length ONT and PacBio: PDF   YOUTUBE
• Practice: ONT   Illumina   YOUTUBE

October 13, 2024 (20h-22h30)

Lecture 26

Shotgun Metagenomics Workflow using Oxford Nanopore Platform

• PDF   YOUTUBE
• PDF_Article   YOUTUBE
• TUTORIAL   YOUTUBE

October 20, 2024 (20h-22h30)

Lecture 27

Introduction Project

• PDF   PPTX   Project

WGS_ONT_Virus

• PDF

Practice

• Mapping   YOUTUBE
• De novo_assembly   YOUTUBE

Pacbio_full_length_16S

• PDF   YOUTUBE
• Tutorial

Practice

• Microbiome 16S   YOUTUBE

  October 27, 2024 (19h-22h30)

Lecture 28

PacBio

• YOUTUBE

ONT

• PDF   Artical   YOUTUBE

November 03, 2024 (20h-22h30)

Lecture 29

Shotgun PacBio

• PDF   YOUTUBE

November 10, 2024 (20h-22h30)

Lecture 30

Denovo + mapping + variant calling PacBio

• PDF
• Practice

References

Books

• R book
• Bioinformatics Linux
• Metagenomics

Some recommended courses for Bash, Scripts, Awk

• Awk  Awk Youtube1  Awk Youtube2
• Scripts