Microbiome Data Analysis Using QIIME2 (MBQM01)
https://www.prinformatics.com/course/microbiome-data-analysis-using-qiime2-mbqm01/
This course will be delivered by Dr. Yoshiki Vazquez Baeza and Dr. Antonio Gonzalez Pena from the 24th - 28th June in Glasgow City Centre.
Course Overview
This course will provide a theoretical, analytical and practical introduction to QIIME 2 (canonically pronounced ‘chime two’), which stands for Quantitative Insights into Microbial Ecology 2, and Qiita (canonically pronounced ‘cheetah’), a multiomics and multi-study online tool. QIIME 2 and Qiita are open source software packages for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic, metabolomics or proteomics). The main Qiita deployment (http://qiita.microbio.me/) allows users to manage and analyze large studies, their metadata and the multiple data types generated from the same samples. Additionally, it allows users to combine their samples with other published and public studies available in the system. QIIME 2 is a stand-alone environment for the analysis of individual microbiome data sets that can be used on your laptop, university computational resources, and cloud computing resources.
Course objectives
By the end of the course, participants will be able to:
- Understand the most recent QIIME2 and Qiita features for microbial community analysis
- Select the best workflow and parameters to perform the different steps for microbial community analysis
- Understand and apply on their own datasets different phylogenetic and non-phylogenetic metrics to compare microbial diversity samples
- Upload and analyze their own datasets using Qiita and compare their studies with other public studies
Course Programme
Monday 24th – Classes from 09:30 to 17:30
Module 1: Introduction to the microbiome.
Module 2 (optional): Refresher of the command line interface and UNIX-like systems.
Module 3: Bioinformatics challenges in the microbiome.
Module 4: Introduction and search for public studies via Qiita.
Tuesday 25th – Classes from 09:30 to 17:30
Module 1: Connecting to workshop server and CLI Refresher.
Module 2: QIIME 2 concepts (artifacts, visualizations, methods, plugins, interfaces, etc).
Module 3: Sample, sequence, and phylogeny processing.
Module 4: Importing and exporting data in QIIME 2.
Wednesday 26th – Classes from 09:30 to 17.30
Module 1: Diversity analyses (alpha diversity).
Module 2: Diversity analyses (beta diversity).
Module 3: Taxonomic classification for target gene data.
Thursday 27th – Classes from 09:30 to 17:30
Module 1: Differential abundance testing.
Module 2: Meta-analyses using Qiita.
Module 3: Creating a study in Qiita.
Module 4: Searching for sequences and environments using redbiom.
Friday 28th – Classes from 09:30 to 16:00
Module 1: Compare the commands and tools we reviewed in the workshop with recent papers.
Module 2: Review other Qiime2 plugins available and tools: PICRUSt, `ili, time series analysis, etc.
Module 3: The Python API for QIIME2.
Module 4: Open science considerations before and after publication.
email oliverhooker@prinformatics.com
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