Untapping diversity through Metagenomics: An Introductory Workshop

Date:

 Monday 3 Thursday 6 December 2018

Venue: 

Universidad de los Andes - UniAndes - Cra 1 Nº 18A - 12, 111711,  Bogota,  CUN, Colombia

Application opens: 

Wednesday October 17 2018

Application deadline: 

Friday November 09 2018

Participation: 

Open application with selection

Registration fee: 

$100,000 COP

Registration closed

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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