REU: Wood Microbiome on Disease vs Healthy Poplar

REU Summer Intership Material

Week 1 [3-7]:

1. Introduction and coding exercises
   1.1 Introduction to the terminal
   1.2 Installing software using the terminal
   1.3 Introduction to R: part 1
   1.4 Introduction to R: part 2
   1.5 Summary of Linux and R \

2. Read Quality Control
   2.1 Check the quality of the reads by using fastqc

   brew install fastqc

   2.2 Check best practices for read quality
   2.3 Report the summary stas for read quality

Week 2 [10-14]:

2. Introduction to Microbiomes
   2.1 What is a microbiome and how to study a microbiome
   2.2 Introduction to metabarcoding
   2.3 Mebarcoding: Illumina reads - sequencing by synthesis
   2.4 Quality assesment
   2.5 Introduction to DADA2

Week 3 [17-21]:

3. Amplicon Sequence Variants (ASVs)
   3.1 Read assesment and ASV generation: part 1
   3.2 Read assesment and ASV generation: part 2
   3.4 Removing chimaeras
   3.5 Weekly summary

Week 4: 24-28

4. Introduction to databases: NCBI nr, UNITE, OomyceteDB, more...
   4.1 Taxonomic assignment and classification
   4.2 Construct a PhyloSeq object 4.3 Plotting taxonomic classification: incidence and abudance
   4.4 Ordination analysis: Non-metric multidimensional scaling
   4.5 Summary results

Week 5: [31-4]

5. Alpha and beta diversity analysis
   5.1 Statistical Analysis of Microbiome Data
   5.2 Analysis testing: part 1
   5.3 Analysis testing: part 2
   5.4 Analysis testing: part 3
   5.5 Summary of analysis testing

Week 6: [7-10]

6. Report
   6.1 Prepare your report
   6.2 Prepare your report and presentation
   6.3 Prepare your presentation and practice
   6.4 Present your work