CBW workshop 2024 beginner

This page is currently a work in progress. It will contain information about the 2024 CBW Beginner Microbiome Analysis: St John's, NL

Module 1: Introduction to sequencing data analysis

• Introduction to Unix
• Introduction to cloud computing (AWS)
• How to install packages in a Unix command line
• Quality control of sequencing data (examining fasta/fastq files) in a Unix command line

Module 2: Marker gene profiling

• 16S analysis workflow using QIIME2 in a Unix command line: initial importing of reads, denoising and ASV generation, taxonomy assignment, filtering of potential contaminants

Module 3: Microbiome statistics and visualizations

• Calculating alpha and beta diversity metrics in QIIME2
• Visualization of sample results using QIIME2
• Calculation of statistically significant differences between groups using QIIME2

Module 4: Functional prediction and additional analyses

• Running PICRUSt2 in Unix command line
• Running differential abundance tests (e.g. ANCOM-II, MaAsLin2, ALDEx2, etc.) in R