Rationale and background:
QIIME 2 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.
- 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 microbiome analysis pipeline. QIIME 2 will address many of the limitations of QIIME 1, while retaining the features that makes QIIME 1 a powerful and widely-used analysis pipeline.
QIIME 2 currently supports an initial end-to-end microbiome analysis pipeline. New functionality will regularly become available through QIIME 2 plugins. You can view a list of plugins that are currently available on the QIIME 2 plugin availability page. The future plugins page lists plugins that are being developed.
This tutorial will orient you to using the QIIME 2 installed on Atmosphere using Jupyter Notebook. This particular demo is adapted from QIIME2 site.
This tutorial will take users through steps of:
- Launching the Qiime-2-Jupyter-notebook Atmosphere image
- Running Qiime-2-Jupyter-notebook on an test data
Part 1: Connect to a Qiime-2-Jupyter-notebook Atmosphere Image (Virtual Machine)
Step 1. Go to https://atmo.cyverse.org and log in with your CyVerse credentials
Step 2. Create a project and name the project name as QIIME2 and description as QIIME2-Jupyter-notebook testing
Step 3. Click the project and then Select the image Qiime-2-jupyter-notebook and click Launch Instance. It will take ~10-15 minutes for the cloud instance to be launched.
Note: Instances can be configured for different amounts of CPU, memory, and storage depending on user needs. This tutorial can be accomplished with the small instance size, medium1 (4 CPUs, 8 GB memory, 80 GB root)
Step 4. Once the VM is ready. Click the VM which will take onto next screen where you can launch web shell
Step 5. Run Jupyter Notebook command for launching Jupyter notebook. The code for running Jupyter-notebook is given below..
Part 2: Running QIIME-2 Jupyter notebook
Step 1. Copy/paste this URL into your browser when you connect for the first time. You should see something like this
Step 2. Click the New tab and then bash kernel to launch new Jupyter notebook page
Step 3. Now you can copy and paste the commands from the below notebook to run Qiime2 moving sample tutorial