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.

Who is this course for?

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:

• 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

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.

What will I learn?

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

Course content

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

Trainers

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 Guilherme Oliveira and Piv Gopalasingam.

Please note that the registration fee of $1300 ARS covers:

• All meals during the course (lunch and refreshment breaks)
• Course materials 
• Course dinner

There will be a maximum of 25 participants on this course and registration is dependent on selection after successful completion of the application process.