Merge pull request #139 from megantranvu/qiime2

QIIME2 Tutorial + Notes

Author: dianalin2

.gitignore

@@ -1,5 +1,6 @@
-.DS_Store
-Thumbs.db
-public/
-.*.swp
-resources/
+.DS_Store
+Thumbs.db
+public/
+.*.swp
+resources/
+venv/

content/notes/qiime2/1_intro.md

@@ -0,0 +1,36 @@
+---
+title: What is QIIME 2?
+date: 2025-06-13-14:45:04Z
+type: docs 
+weight: 50
+menu: 
+    qiime2:
+---
+
+[QIIME 2](https://qiime2.org) is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.
+
+{{< figure src=/notes/qiime2/img/logo.png width=70% height=70% >}}
+
+
+__Key features:__
+
+  * Integrated and automatic tracking of data provenance
+  * Semantic type system
+  * Plugin system for extending microbiome analysis functionality
+  * Support for multiple types of user interfaces (e.g. API, command line, graphical)
+
+
+QIIME 2 is a complete redesign and rewrite of the [QIIME 1](http://qiime.org/) microbiome analysis pipeline. QIIME 2  addresses many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.
+
+__High-level features:__
+
+* Latest and greatest microbiome bioinformatics methods and visualizations
+* Accessibility through accurate, detailed, and interesting documentation and well-designed interfaces
+* A community of microbiome scientists, developers, and bioinformaticians
+
+
+__Interfaces__
+
+QIIME 2 has many available interfaces. Choose the interface that helps you work most efficiently.
+
+{{< figure src=/notes/qiime2/img/interfaces.png width=70% height=70% >}}

content/notes/qiime2/2_qiime_core.md

@@ -0,0 +1,42 @@
+---
+title: QIIME 2 Core 2022.8 Distribution
+date: 2025-06-13-14:45:04Z
+type: docs 
+weight: 100
+menu: 
+    qiime2:
+---
+
+The QIIME 2 Core 2022.8 distribution includes the QIIME 2 framework, q2cli (a QIIME 2 command-line interface), and the following plugins:
+
+* q2-alignment
+* q2-composition
+* q2-cutadapt
+* q2-dada2
+* q2-deblur
+* q2-demux
+* q2-diversity
+* q2-diversity-lib
+* q2-emperor
+* q2-empress
+* q2-feature-classifier
+* q2-feature-table
+* q2-fragment-insertion
+* q2-gneiss
+* q2-longitudinal
+* q2-metadata
+* q2-phylogeny
+* q2-picrust2
+* q2-quality-control
+* q2-quality-filter
+* q2-sample-classifier
+* q2-taxa
+* q2-types
+* q2-vsearch
+
+
+The QIIME 2 Core 2022.8 distribution includes plugins and interfaces that are developed, maintained, tested, and distributed by the QIIME 2 development team. The Core distribution is necessary to run the commands in the QIIME 2 tutorials. If there are additional QIIME 2 plugins or interfaces you would like to install, please consult the relevant package(s) documentation. Other types of distributions may be made available in the future in addition to Core.
+
+{{< figure src=/notes/qiime2/img/cli.png caption="The QIIME 2 command-line interface helps you work on Rivanna." width=70% height=70% >}}
+
+

content/notes/qiime2/3_importing_data.md

@@ -0,0 +1,20 @@
+---
+title: Importing Data
+date: 2025-06-13-14:45:04Z
+type: docs 
+weight: 150
+menu: 
+    qiime2:
+---
+
+Data produced by QIIME 2 exist as **QIIME 2 artifacts**. A QIIME 2 artifact contains data and metadata. The metadata describes things about the data, such as its type, format, and how it was generated (provenance). A QIIME 2 artifact typically has the .qza or .qzv file extension when stored in a zip file.
+
+Since QIIME 2 works with artifacts instead of data files (e.g. FASTA files), you must create a QIIME 2 artifact by importing data. You can import data at any step in an analysis, though typically you will start by importing raw sequence data. QIIME 2 also has tools to export data from an artifact. See the [QIIME 2 Importing Guide](https://docs.qiime2.org/2022.8/tutorials/importing/) for details on how to import data.
+
+Note: if you are having trouble unzipping the file, you can run this line in your command line.
+```bash
+qiime tools extract
+```
+
+For more information, visit [https://dev.qiime2.org/latest/storing-data/](https://dev.qiime2.org/latest/storing-data/
+)

content/notes/qiime2/4_view_results.md

@@ -0,0 +1,19 @@
+---
+title: View QIIME 2 Results
+date: 2025-06-13-14:45:04Z
+type: docs 
+weight: 250
+menu: 
+    qiime2:
+---
+
+[QIIME 2 View](https://view.qiime2.org) is a read-only web interface that can be used to view QIIME 2 results, even if you don't have QIIME 2 installed.
+
+{{< figure src=/notes/qiime2/img/view.png width=70% height=70% >}}
+
+__Features:__
+* Reads QIIME 2 outputs (QZAs and QZVs)
+* No installation required
+* Easily share links using Dropbox with collaborators
+* No uploading (your data stays on your computer)
+

content/notes/qiime2/5_practice.md

@@ -0,0 +1,20 @@
+---
+title: Hands-On Practice
+date: 2025-06-13-14:45:04Z
+type: docs 
+weight: 300
+menu: 
+    qiime2:
+---
+
+Copy the following files to your home directory:
+
+```bash
+cp -rp  /project/rivanna-training/singularity_qiime2 ./
+```
+
+Then submit the job to run:
+
+```bash
+sbatch q2-import.slurm
+```

content/notes/qiime2/_index.md

@@ -0,0 +1,17 @@
+---
+title: Introduction to QIIME 2
+date: 2025-6-10T00:00:00-05:00
+authors: []
+type: docs 
+weight: 1 
+date: 2025-6-10T00:00:00-05:00
+
+menu: 
+    qiime2:
+---
+
+
+In this tutorial, we will be discussing the following topics:
+* What is QIIME 2
+* How to import data into QIIME 2
+* How to view QIIME 2 results