Resources¶
Downloads
Workshop Files
Data files, manifests, metadata, classifiers, and R scripts, everything needed to follow along on Alpine HPC.
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Glossary
Key Terms
Searchable definitions for metrics, methods, and file formats used throughout the workshop.
Browse Glossary
Publication Plots in R
Self-Study
Full export reference for moving QIIME2 artifacts into R, plus the workshop's
Open Reference
visualizations.Rmd setup for publication-quality figures.Installing QIIME2
Setup Guide
Reference for installing QIIME2 and verifying the installation before the workshop.
Open Guide
Scripting and Submitting Jobs on Alpine
Reference
Reference for writing scripts and submitting jobs on Alpine.
Open Guide
Filtering Long Amplicons
Reference
Remove off-target, overly long amplicons (e.g. 18S reads picked up by the 16S primers) from your representative sequences.
Open Reference
Transferring Files to Alpine
Globus & Data Transfer
Move large or numerous files to Alpine with GlobalProtect and Globus, including linking external storage like OneDrive or Dropbox.
Open Guide
Uploading 16S Data to Qiita
Data Sharing
Submit your 16S sequences and metadata to Qiita, with the workshop SOP and a metadata template to get you started.
Open Guide
Further Reading¶
| Resource | Description |
|---|---|
| QIIME2 Documentation | Official QIIME2 plugin and tutorial reference |
| QIIME2 Forum | Community support and Q&A |
| GreenGenes2 | Reference taxonomy and tree resources |
| DADA2 Paper | Callahan et al. 2016, original DADA2 publication |
| ANCOM-BC Paper | Lin & Peddada 2020, original ANCOM-BC publication |
| UniFrac Paper | Lozupone & Knight 2005, UniFrac distance metric |
Useful Tools¶
| Tool | Description |
|---|---|
| QIIME2 View | Browser-based viewer for .qzv visualization files |
| Microbiome Analyst | Web-based downstream analysis platform |
| phyloseq | R package for microbiome data analysis |
| vegan | R package for community ecology statistics |
Citation¶
If you use methods or materials from this workshop in your research, please cite QIIME2:
Bolyen E, Rideout JR, Dillon MR, et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9