CABANA Workshop: Untapping diversity through Metagenomics: An Introductory Workshop
The application system requires cookies, and the limited processing of your personal data in order to function. By applying to this course you are agreeing to this as outlined in our Privacy Notice and Terms of Use
Date:
Monday 3 - Thursday 6 December 2018Venue:
Universidad de los Andes - UniAndes - Cra 1 Nº 18A - 12, 111711, Bogota, CUN, ColombiaApplication opens:
Wednesday 17 October 2018Application deadline:
Friday 09 November 2018Participation:
Open application with selectionRegistration fee:
$100,000 COPRegistration closed
Course Overview
In this course participants will learn the basics of metagenomics, covering experimental design and workflows, moving through to microbiome analysis via amplicon sequencing and shotgun metagenomics. The course theme will be biodiversity, with relevant examples and use cases applied throughout.
The course will be delivered by experienced and dedicated world-renowned experts, including EMBL-EBI trainers, and will involve presentations, demonstrations and practical exercises to give participants hands-on experience.
Audience
This course is suitable for postgraduate wet-lab researchers at any career stage within Latin America who are working with and/or generating their own metagenomics datasets.
Participants will require a basic knowledge of the Unix command line, and the R statistical packages. We recommend these free tutorials:
Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
Introduction and exercises for Linux: https://training.linuxfoundation.org/free-linux-training
Basic R concept tutorials: www.r-tutor.com/r-introduction
A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.
Modules
- european-nucleotide-sequence-archive-ena
Learning outcomes
After this course you should be able to:
- Access and submit data to public resources for metagenomics
- Determine comparative taxonomic content of different samples
- Determine comparative functional capacities of different samples
- Run different clustering methods
Programme
Day 1 – Monday 3 December 2018 |
||
|---|---|---|
| 08:00 - 08:30 | Arrival, registration, refreshments | |
| 08:30 - 09:30 | Welcome and introduction to Metagenomics | Alejandro Reyes |
| 09:30 - 10:30 | European Nucleotide Archive | ENA team |
| 10:30 - 11:00 | Break | |
| 11:00 -12:30 | European Nucleotide Archive (hands-on) | ENA team |
| 12:30 - 14:00 | Lunch | |
| 14:00 - 15:30 | Experimental design in metagenomics | Scott Handley |
| 15:30 - 16:00 | Break | |
| 16:00 - 17:00 | Metagenomics workflows; basic R environment for metagenomics | Scott Handley |
| 17:00 - 18:00 | An overview of data analysis, statistics and quality control in metagenomics | Scott Handley |
| 18:00 | End of day 1 | |
Day 2 – Tuesday 4 December 2018 |
||
|---|---|---|
| 09:00 - 10:30 | American Gut Project and Earth Microbiome Project; Introduction to QIIME | Daniel McDonald |
| 10:30 - 11:00 | Break | |
| 11:00 - 12:30 | QIIME2: Differences and Improvements from QIIME1. Quality Control, Importing and Demultiplexing | Daniel McDonald |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | QIIME2; OTUs and Sequence Variants, Phylogeny, Rarefaction | Daniel McDonald |
| 15:00 - 15:30 | Break | |
| 15:30 - 17:00 | QIIME2: Diversity analyses (alpha and beta), metrics, visualization and other QIIME analysis tools | Daniel McDonald |
| 17:00 | End of day 2 | |
Day 3 – Wednesday 5 December 2018 |
||
| 08:00 - 09:30 | MGnify | Alex Mitchell/Rob Finn (webinar) + Guillermo Rangel (F2F) |
| 09:30 - 10:00 | Break | |
| 10:00 - 11:30 | MGnify | Alex Mitchell/Rob Finn (webinar) + Guillermo Rangel (F2F) |
| 11:30 - 12:00 | Protein Database | Alex Mitchell/Rob Finn (webinar) + Guillermo Rangel (F2F) |
| 12:00 - 13:30 | Lunch and poster session | |
| 13:30 - 15:00 | Keynote lecture/worked examples of metagenomics bioinformatics | TBC |
| 15:00 - 15:30 | Break | |
| 15:30 - 17:00 | R- Advanced statistics for the microbiome | Scott Handley |
| 17:00 | End of day 3 | |
Day 4 – Thursday 6 December 2018 |
||
| 09:00 - 10:30 | Shotgun metagenomics: Applications | Bent Petersen |
| 10:30 - 11:00 | Break | |
| 11:00 - 12:30 | Shotgun metagenomics: Assembly (hands-on) | Bent Petersen |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Shotgun metagenomics: Genome annotation (hands-on) | Bent Petersen |
| 15:00 - 15:30 | Break | |
| 15:30 - 16:30 | Shotgun metagenomics: Binning (hands-on) | Bent Petersen |
| 16:30 - 17:00 | Course close and feedback | Alejandro Reyes |
In association with
How to apply
In order to be considered for a place on this course applicants must complete the online application form.
Incomplete applications will NOT be considered.
If you have any queries about the registration process please email Piv Gopalasingam.
The registration fee includes:
- Tea/coffee and lunches will be provided for the duration of the course
- Course dinner on Thursday 6th December
- Use of the course training room
- Course materials provided
- Course certificate
Application deadline
09 November 2018
Number of places
30 places
Organisers
Alejandro Reyes - Universidad de los Andes
Guilherme Oliveira - Instituto Tecnológico Vale - ITV - Vale Technological Institute
Piraveen Gopalasingam - EMBL-EBI, UK
Trainers
Alejandro Reyes - Universidad de los Andes
Daniel McDonald - University of California San Diego
Bent Petersen - Technical University of Denmark
Scott Handley - Washington University School of Medicine in St. Louis
Guillermo Rangel - EMBL-EBI, UK