CABANA Workshop: Introduction to Metagenomics

Date:

 Monday 2 Friday 6 December 2019

Venue: 

Faculty of Natural Sciences - University of Buenos Aires (FCEN-UBA) - Ciudad Universitaria. Nuñez - Ciudad Autónoma de Buenos Aires - Pabellón II, 1428,  Buenos Aires,  Buenos Aires, Argentina

Application opens: 

Tuesday 03 September 2019

Application deadline: 

Sunday 29 September 2019

Participation: 

Open application with selection

Contact: 

Derrin Crawte, Maria Bernardi

Registration fee: 

ARS $1300

Registration closed

Find other similar courses »

Course Overview

In this course participants will learn the basics of metagenomics, covering experimental design and workflows, moving through to microbiome analysis via metabarcoding and shotgun metagenomics. The course theme will be the use of metagenomics oriented to biodiversity.

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.

Syllabus, Tools and Resources

During this course you will learn about: 

  • Basic Unix and R environment for metagenomics
  • FastQC for Quality control and Trimmomatic for preprocessing
  • MGnify annotation pipeline for Metabarcoding
  • SPAdes and metaSPAdes for assembly, metaWRAP for binning
  • InterProScan and Genome Properties for genome and metagenome annotation
  • R tools for metagenomics analyses such as dada2, Phyloseq, ggplot2 and gggenes

Audience

This course is suitable for postgraduate wet-lab researchers and also bioinformaticians at graduate-level upwards within Latin America who are working with and/or generating their own metagenomics datasets. 

Prerequisites: 
Undergraduate-level knowledge of biology would be advantageous. Participants will also require a basic knowledge of the Unix command line, and the R statistical packages. We recommend these free tutorials:

Please note this course will be taught in English, however the trainers are fluent in either Spanish, and can offer language support where feasible.

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.
 

Learning outcomes

After this course you should be able to:

  • Use Unix and R tools for metagenomics analyses
  • Process metagenomics data
  • Use metagenomics databases
  • Annotate genome and metagenomes
  • Analyse metagenomic results

Programme

Day 1: Introduction to NGS methods, metagenomics workflow, basic Unix and R, quality control and preprocessing.

Day 2: Metabarcoding and MGnify 

Day 3: Genome assembly, metagenomes and binning

Day 4: Genome and metagenome annotation, EMBL-EBI resources for metagenomics (InterProScan, Genome Properties)

Day 5: Applications of metagenomics, further analysis and interpretation

 

A full programme will be provided shortly.