Explore microbiome bioinformatics through a comprehensive 12-hour online workshop focused on QIIME 2. Gain a high-level introduction to QIIME 2, understanding semantic types and data formats. Refresh your knowledge of Linux File System and Command Line Interface. Dive into the PD Mice study, learning about sample metadata, 16S lab protocols, and how to share analysis results using QIIME 2 View. Master techniques for importing, demultiplexing, and denoising sequences, as well as phylogenetic reconstruction and taxonomic assignment. Delve into rarefaction, core metrics, and diversity analyses, including alpha and beta diversity visualizations. Explore differential abundance testing using ANCOM, sample classification, and longitudinal analyses. Conclude with a synthesis of the PD Mice study, equipping you with practical skills in microbiome data analysis using QIIME 2.
Overview
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.
Taught by
QIIME 2
