Microbiome Bioinformatics with QIIME 2 - Online Workshop

This workshop introduces QIIME 2 for microbiome bioinformatics, using 16S sequence data and a mouse study to demonstrate metadata handling, sequence processing, phylogenetic reconstruction, taxonomic analysis, diversity metrics, differential abundance, classification, and longitudinal analyses.

Syllabus

A high-level introduction to QIIME 2.
Semantic types and data formats in QIIME 2.
Linux File System and Command Line Interface Refresher.
PD Mice: Study background and information.
Sample Metadata.
PD Mice: Sample Metadata.
16S Lab protocols.
Sharing your analysis results with collaborators using QIIME 2 View.
Importing and demultiplexing.
PD Mice: Importing demultiplexed sequences.
Denoising.
PD Mice: Denoising.
PD Mice: Phylogenetic reconstruction.
Phylogenetic reconstruction.
Taxonomic assignment.
PD Mice: Taxonomic classification.
Rarefaction.
PD Mice: Even Sampling Depth.
PD Mice: Core metrics phylogenetic tutorial.
Alpha diversity metrics.
PD Mice: Alpha diversity visualizations.
Beta diversity metrics.
PD Mice: Beta diversity visualizations.
Differential Abundance Testing.
PD Mice: ANCOM differential abundance testing.
Sample classification.
PD Mice: Sample classification.
Longitudinal analyses.
PD Mice: Longitudinal Analyses.
PD Mice: Synthesis.