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QIIME 2 Cancer Microbiome Intervention Tutorial

Getting started with QIIME 2

Getting started with using QIIME 2

Upstream tutorial

Hematopoietic cell transplantation data
Exploring the tutorial metadata
Importing demultiplexed sequence data
Denoising sequence data with DADA2

Downstream tutorial

Filtering feature tables
Taxonomic annotation of observed sequences
Phylogenetic tree construction
Identifying an even sampling depth for use in diversity metrics
Computing diversity metrics
Alpha diversity visualizations
Beta diversity visualizations
Longitudinal microbiome analysis
Provenance in QIIME 2

Appendices

Import figshare data into QIIME 2 artifacts
Access and explore figshare sample and patient metadata
Human sequence read filtering from fastq files
List of works cited

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By The QIIME 2 Developers

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