QIIME Tutorials

The QIIME tutorials are documents that illustrate how to use various features of the QIIME. We recommend that all users begin with the QIIME overview tutorial which takes the user through a full analysis of sequencing data. After you’ve begun analyzing your own data, you’ll want to move on to the special-purpose tutorials as needed.

The QIIME development team is very interested in incorporating community-contributed tutorials. Please contact the QIIME Forum if you’re interested in contributing.

Getting started: Sequence processing through OTU tables and phylogenetic trees

• OTU picking strategies in QIIME
• Illumina Overview Tutorial (an IPython Notebook): open reference OTU picking and core diversity analyses
• 454 Overview Tutorial: de novo OTU picking and diversity analyses using 454 data
• Discussion of subsampled open reference OTU picking in QIIME
• Fungal ITS analysis tutorial (an IPython Notebook): open-reference OTU picking
• Preparing raw Illumina data in different formats for use with QIIME
• Analysis of 18S data
• Working with BIOM tables in QIIME

Additional Quality Control

• Denoising of 454 Data Sets
• Chimera checking sequences with QIIME
• Using usearch quality filtering with QIIME
• Denoising and chimera detection usage differences in QIIME

Alternative Processing Steps

• Taxonomic classifications of single- and paired-end sequences with RTAX
• Re-training the RDP Classifier
• Predicting Mislabeled Samples
• Filtering contaminant or category specific OTUs from OTU tables
• Multi-step OTU picking
• Extracting Barcodes from fastq data for compatibility with split_libraries_fastq.py

Analyzing diversity

• Comparing Categories
• Creating Distance Comparison Plots
• Comparing Distance Matrices
• Comparing Taxa Summaries
• Making Cytoscape Networks
• Running Supervised Learning
• Performing Procrustes Analysis
• Tracking the source of microbes with SourceTracker

Experimental QIIME features: these tutorials cover features that should be considered beta QIIME software

• Analysis of shotgun sequencing data

Other

• Basic Unix/Linux/OS X commands
• Working with QIIME on Amazon Web Services EC2
• Using parallel QIIME
• Using Remote Mapping Files
• Describing samples based on their metadata