Tutorials¶
Note
The tutorials assume you have installed the QIIME 2 Amplicon Distribution using one of the procedures in the install documents. The tutorials make extensive use of the QIIME 2 command-line interface so reviewing the q2cli docs is recommended.
- Overview of QIIME 2 Plugin Workflows
- QIIME 2 for Experienced Microbiome Researchers
- “Moving Pictures” tutorial
- Sample metadata
- Obtaining and importing data
- Demultiplexing sequences
- Sequence quality control and feature table construction
- FeatureTable and FeatureData summaries
- Generate a tree for phylogenetic diversity analyses
- Alpha and beta diversity analysis
- Alpha rarefaction plotting
- Taxonomic analysis
- Differential abundance testing with ANCOM-BC
- “Moving Pictures” tutorial - Multiple Interface Edition
- Beta preview note
- Introduction
- Sample metadata
- Obtaining and importing data
- Demultiplexing sequences
- Sequence quality control and feature table construction
- FeatureTable and FeatureData summaries
- Generate a tree for phylogenetic diversity analyses
- Alpha and beta diversity analysis
- Alpha rarefaction plotting
- Taxonomic analysis
- Differential abundance testing with ANCOM-BC
- Fecal microbiota transplant (FMT) study: an exercise
- “Atacama soil microbiome” tutorial
- Parkinson’s Mouse Tutorial
- Hypothesis
- Set up
- Metadata
- Importing data into QIIME 2
- Sequence quality control and feature table
- Generating a phylogenetic tree for diversity analysis
- Alpha Rarefaction and Selecting a Rarefaction Depth
- Diversity analysis
- Taxonomic classification
- Taxonomy barchart
- Differential abundance with ANCOM-BC
- Taxonomic classification again
- Longitudinal analysis
- Machine-learning classifiers for predicting sample characteristics
- Synthesis
- Importing data
- Sequence data with sequence quality information (i.e. FASTQ)
- Sequences without quality information (i.e. FASTA)
- Per-feature unaligned sequence data (i.e., representative FASTA sequences)
- Per-feature aligned sequence data (i.e., aligned representative FASTA sequences)
- Feature table data
- Phylogenetic trees
- Other data types
- Exporting data
- Metadata in QIIME 2
- Filtering data
- Training feature classifiers with q2-feature-classifier
- Evaluating and controlling data quality with q2-quality-control
- Predicting sample metadata values with q2-sample-classifier
- Performing longitudinal and paired sample comparisons with q2-longitudinal
- Pairwise difference comparisons
- Pairwise distance comparisons
- Linear mixed effect models
- Volatility analysis
- First differencing to track rate of change
- Tracking rate of change from static timepoints
- Non-parametric microbial interdependence test (NMIT)
- Feature volatility analysis
- “Maturity Index” prediction
- Identifying and filtering chimeric feature sequences with q2-vsearch
- Alternative methods of read-joining in QIIME 2
- Clustering sequences into OTUs using q2-vsearch
- Utilities in QIIME 2
- Phylogenetic inference with q2-phylogeny