QIIME 2 Workshop
General Information
Date: July 22th - 23th 2021
Timetable: 8:00 - 17:00 h GTM-5.
Language: English
Participants: Limited to 30 participants. Registration occurs on a selection based on the justification and need
Registration fee: USD 35
Deadline applications: June 30
Version: Online
Description
Members of the Research Group in Computational Biology and Microbial Ecology, from Universidad de los Andes in Bogotá, Colombia, with support from the QIIME 2 team, will teach a two-day online workshop on bioinformatics tools for microbiome science in the context of the Latin American ISME conference held virtually on 2021. The workshop will include lectures covering theory and usage of QIIME 2, and practical work with QIIME 2 to perform microbiome analysis from raw sequence data through publication-quality statistics and visualizations. This online course will comprise a blend of pre-recorded and live lectures. Pre-recorded lectures will be made available prior to each day of the workshop, that way attendees with schedule conflicts can stay caught up with the material. There will also be interactive command-line based tutorial sessions, where attendees will perform microbiome analyses using QIIME 2, online. We will also host live question-and-answer sessions, as well as general discussion sessions.
Topics
- Introduction to QIIME 2
- Core concepts
- QIIME 2 types, formats, and metadata
- Demultiplexing and quality control
- Phylogenetic reconstruction
- Measuring alpha and beta diversity
- Importing and exporting data
- Taxonomic analysis
- Differential abundance
- QIIME 2 plugin highlights
- And more!
Attendee requirements
Students will use the Linux command line extensively during the hands-on portion of the workshop. We will not cover command-line usage in this workshop and thus it is strongly encouraged that you become familiar with the command line prior to the workshop. We will share a couple of online tutorials and videos previous to the workshop that will help.
Technical and computational requirements
- Before the workshop, please install the latest version of the Google Chrome web browser. If you do not have Google Chrome installed, get it here.
Students will be given access to a virtual machine and a username in order to complete the hands-on portion of the workshop. In order to connect to the virtual machine, students are invited to download Google Chrome Secure Shell App for SSH and CyberDuck for SFTP. If you have enough experience and have a preferred SSH or SFTP tool you can use it as well, but we may not be able to support in case of questions regarding the tool use.
Preparation for the course
- Command line interface tutorial
- Original Paper on QIIME2
- Core concepts explanation. Available here
- Overview of QIIME 2 Plugin Workflows: Available here
Schedule
Hours GTM-5 |
Day 1 |
Day 2 |
|---|---|---|
| 8:00 - 8:30 | Welcome and Introduction * | Rarefaction |
| 8:30 - 9:30 | Semantic types and data format | Alpha diversity and Alpha group significance |
| 9:30 - 10:00 | Break | Break |
| 10:00 - 11:30 | Connecting to servers | Beta diversity and Beta group significance |
| Metadata files, importing and demultiplexing | ||
| 12:00 - 13:00 | Lunch Break | Lunch Break |
| 13:00 - 14:30 | Denoising | Taxonomic Assignment |
| 14:30 - 14:40 | Break | Break |
| 14:40 - 16:00 | Phylogenetic reconstruction | Showcase: Differential abundance |
| 16:00 -16:10 | Break | Break |
| 16:10 - 17:00 | General Questions | General Questions and closing * |
* Prof Caporaso and other QIIME 2 developers will be in attendance for some sessions
Instructors
BCEM
Maryam Chaib De Mares, PhD
Luis Alberto Chica
Nickole Villabona
Leda Restrepo
Alejandro Reyes Muñoz, PhD
The following members of the QIIME 2 team will join workshop sessions indicated above with an asterisk:
Specifically, Dr. Caporaso will give an opening lecture, and all members of this group will answer questions in the closing Q&A session.
Note:
- If you are selected to attend this course, you will be informed on July 10th, to the email address provided.
If you have any questions about this course, send us an email at: ismelatinoamerica@gmail.com
Register for this course Here
