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Microbiome Data Analysis Using QIIME2 (MBQM01)
24 June 2019 - 28 June 2019£275.00 - £570.00
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.
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
This workshop is aimed at all researchers and technical workers with a background in biology who want to build pipelines for DNA from microbial communities.
Venue – PR informatics head office, 53 Morrison Street, Glasgow, G5 8LB – Google map
Availability – 25 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English
We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments and welcome meal Monday evening.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, refreshments and welcome dinner Monday evening. Self-catering facilities are available in the accommodation. Accommodation is approximately a 6-minute walk from the PR informatics head office. Accommodation is multiple occupancy (max 3-4 people) single sex en-suite rooms. Arrival Sunday 23rd June (between 17:00 – 21:00 and departure Friday 28th June (accommodation must be vacated by 09:15).
To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.
Other payment options are available please email email@example.com
PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact firstname.lastname@example.org. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees (and accommodation fees if booked through PR informatics) will be credited. However, PR informatics will not be held responsible/liable for any travel fees, accommodation costs or other expenses incurred to you as a result of the cancellation. Because of this PR informatics strongly recommends any travel and accommodation that is booked by you or your institute is refundable/flexible and to delay booking your travel and accommodation as close the course start date as economical viable.
The workshop is delivered over five full-day sessions. Each session consists of two 3 and half hour sessions, with breaks at the organizer’s discretion. Each session uses examples and exercises that build on material from the previous one, so it’s important that students attend all sessions. A description of the sessions can be found under programme.
Assumed computer background
No computer background assumed. However, students should be familiar with the use of the command line interface but it’s not required as we can have a quick introduction as part of day 1 module 2 (depending on the students’ background experience).
Equipment and software requirements
Please bring your laptop to the workshop, as a significant portion of the workshop will be hands-on. Any operating system will work, including Windows, Mac OS X, and Linux. You do not need to install any other software besides what is listed below. There will be power outlets and WiFi available to you at the workshop.
Before the workshop, please install the latest version of the Google Chrome web browser. If you don’t have Google Chrome installed, get it here. If you already have Google Chrome installed, make sure it is the latest version by following these instructions. Next, install the Secure Shell app for Google Chrome. Next, try to open this page to ensure that your browser is configured correctly to view Emperor plots. If you get a notice that the page cannot be opened, follow the instructions and try the link again. Finally, if you are using Windows or Mac OS X, install Cyberduck.
If you plan to bring your own dataset, which we highly encourage, to the workshop the requirements are that (1) you upload your sample & preparation templates, (2) and raw data to Qiita. If you run into any issue send an email to email@example.com
UNSURE ABOUT SUITABLILITY THEN PLEASE ASK firstname.lastname@example.org
Meet at 43 Cook Street, Glasgow G5 8JN at approx. 17:00 onwards
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.