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.
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.
Basic Unix and R knowledges. Bring your own device principle (BYOD), means a laptop with sufficient capabilities (8GB RAM, WIFI) is needed (no tablet!).
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.
Unix&SLURM refresh & RStudio refresh
OS Lectura, Unix tutorial
Introduction to sequencing technologies, short and long reads (LF or IMG) Lecture
Quality Control and cleaning of the reads
Principles and advantages, choice of primers, OTU vs ASV (LF)
RStudio use of the DADA2 packageDownstream analyses (JYG) Lecture, Practical
RStudio with the PhyloSeq and other packages Lecture, Practical
APrinciples and advantages, choice of the sequencing technique
Taxonomic classification, contaminant removalKraken/Bracken Lecture, Practical
SComparing Pipelines, workflow managers (i.e SnakeMake, Nextflow) Lecture, Practical
QC+Assembly+Binning, co-assembly, co-binning, evaluations BUSCO/CheckM2, QUAST, GUNC, GTDBTK-2.
Downstream analyses, gene prediction, annotation, function, pathway eggNOG, KEGG, AntiSmash
Data submission and PublicationLecture, Practical
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
Basic Unix and R knowledge. Bring your own device principle (BYOD).
It is a no-profit course, and the fee will cover only the direct course expenses.
Universidad Nacional de Colombia student | $250.000 |
Student | $300.000 |
Others | $350.000 |
ContactEmiliano Barreto-HernándezProfesor Asociado, PhD. Instituto de Biotecnología - Universidad Nacional de Colombia Sede Bogotá ebarretoh@unal.edu.co Tel: +57 3165000 ext 16976 Fax +571 3165415 |