QIIME 2 Cancer Microbiome Intervention Tutorial

This tutorial guides learners through a QIIME 2 workflow for cancer microbiome sequencing data, including data import, DADA2 denoising, taxonomic assignment, phylogenetic reconstruction, diversity analysis, longitudinal analysis, and sample classification.

Syllabus

Introduction to the QIIME 2 Cancer Microbiome Intervention video tutorial.
An introduction to QIIME 2.
Running QIIME 2 inside Galaxy (alpha release version).
QIIME 2 Galaxy introduction.
Semantic types and data formats in QIIME 2.
Introduction to the Cancer Microbiome Intervention Tutorial data.
Sample Metadata.
Exploring the tutorial metadata.
Importing and demultiplexing.
16S Lab protocols.
Importing demultiplexed sequence data.
Denoising.
Denoising sequence data with DADA2.
Filtering feature tables.
Taxonomic assignment.
Taxonomic annotation of observed sequences.
Phylogenetic reconstruction.
Phylogenetic tree construction.
Rarefaction.
Identifying an even sampling depth.
Computing diversity metrics.
Alpha diversity metrics.
Alpha diversity visualizations.
Beta diversity metrics.
Beta diversity visualizations.
Longitudinal analyses.
Longitudinal microbiome analysis.
Sample classification.