Sequencing technology advances have opened the field of metagenomics, enabling the exploration of microbial communities in various environments, thanks to bioinformatics analysis algorithms and pipelines. Uncovering the versatility of metagenomics in various domains is an essential step for environmental studies, agriculture, and human health. In particular the mixture of fungi and bacteria for creating synthetic communities is an emerging field of interest in many countries with a focus on crop health, soil microbiota, and rhizosphere interactions.

The workshop will conclude with a mini-symposium that aims to highlight some real-life analysis workflows and results. This could potentially open enthusiastic perspectives and collaborations between lab and field researchers, expert bioinformaticians, and other interested scientists in agriculture and human health.

Organizadores

 

 

 

 

 

 

Workshop Objectives

1. To cover the metagenomics data analysis workflow from data generation to publication.

2. To explore the tools to manage, share, analyze and interpret metagenomics data.

Workshop Prerequisites

Basic Unix and R knowledges. Bring your own device principle (BYOD), means a laptop with sufficient capabilities (8GB RAM, WIFI) is needed (no tablet!).

Workshop Methodology

The course workflow will be based on lectures taught by the invited instructor in combination with hands-on exercises for computational processing and analysis. Teaching assistants will be available in the room for guidance during the hands-on exercises. Additionally, some participants will have the chance to present their work and data analysis. The workshop will cover the following topics: Issues of data quality control and how to process the data until publication, both targeted marker-gene and whole-genome shotgun (WGS) approaches with a primary focus on assembly-based approaches, explore considerations when assembling metagenomics data, the analysis that can be carried out, and what downstream analysis options and tools are available.

 

 

 

 

 

 

 

 

Program

Unix

Jun 17. Introduction and refresh

AM

Introduction to Metagenomics, goals and opportunities (JYG or LF or IMG)

Unix&SLURM refresh & RStudio refresh

OS Lectura, Unix tutorial

PM

Introduction to sequencing technologies, short and long reads (LF or IMG) Lecture

Quality Control and cleaning of the reads

De Novo

Jun 18. Targeted sequencing

AM

Principles and advantages, choice of primers, OTU vs ASV (LF)

RStudio use of the DADA2 package

PM

Downstream analyses (JYG) Lecture, Practical

RStudio with the PhyloSeq and other packages Lecture, Practical

Anotation

Jun 19. WGS sequencing part I (JYG)

AM

APrinciples and advantages, choice of the sequencing technique

Taxonomic classification, contaminant removal

Kraken/Bracken Lecture, Practical

pM

SComparing Pipelines, workflow managers (i.e SnakeMake, Nextflow) Lecture, Practical

QC+Assembly+Binning, co-assembly, co-binning, evaluations BUSCO/CheckM2, QUAST, GUNC, GTDBTK-2.

 

Comparative

Jun 20. WGS sequencing part II (LF or IMG)

AM

Downstream analyses, gene prediction, annotation, function, pathway eggNOG, KEGG, AntiSmash

Data submission and Publication

Lecture, Practical

PM

Individual questions and discussions
Clinical

Jun 21. Mini-symposium

Invited speaker talks

Prof. Esperanza Torres Universidad Nacional de Colombia

Prof. Pilar Junier Université de Neuchâtel

PhD Vannesa  Otero

PhD Ivan Mateus

 

Participant short talks

 

 

 

 

 

 

Team

PhD. Emiliano Barreto-Hernandez

Organizer

PhD. Laurent Falquet

Invited Professor

PhDc. Jeferyd Yepes-Garcia

Invited Professor

PhD. Ivan Mateus Gonzalez

Invited Professor

 

 

 

 

 

 

Pre-requisities: 

Basic Unix and R knowledge. Bring your own device principle (BYOD).

Registration fee 

It is a no-profit course, and the fee will cover only  the direct course expenses.

Fees table 

Universidad Nacional de Colombia  student  $250.000
 Student  $300.000
 Others  $350.000

Contact

Emiliano Barreto-Hernández
Profesor Asociado, PhD.
Instituto de Biotecnología - Universidad Nacional de Colombia Sede Bogotá
ebarretoh@unal.edu.co
Tel: +57 3165000 ext 16976 Fax +571 3165415