This course will cover the metagenomics data analysis workflow from data generation to downstream analysis. Participants will explore the tools to manage, share, analyze and interpret metagenomics data. The content will include issues of data quality control and how to process the data until publication.
Both targeted marker-gene (eg., 16S) and whole-genome shotgun (WGS) approaches will be covered. Discussions will also explore considerations when selecting the sequencing options (long or short reads), exploring targeted data to OTUs or ASVs, assembling and binning metagenomics data, the analyses that can be carried out , and what downstream analyses options and tools are available.
This course is aimed at life scientists (PhD or postdocs) who are working in the field of metagenomics and are currently in the early stages of data preparation or data analysis.
The participants will be:
- Learning the concepts of metagenomics
- Understanding and comparing the two main methods (targeted vs whole genome)
- Performing QC and cleaning of the data
- Learning about various databases and pipelines
- Evaluating the results of the pipelines
- Discovering downstream analysis options
The practical sessions in the course require a basic understanding of the Unix command line and the R statistics packages. Participants might want to work through these free tutorials before attending the course:
Basic introduction to the Unix environment:
https://www.sib.swiss/training/course/2012_UNIXF
General concepts to schedule jobs using SLURM:
https://hprc.tamu.edu/wiki/FASTER:Batch#Job_Submission
Basic R concept tutorials:
https://moderndive.netlify.app/1-getting-started.html
- Enseignant·e: Laurent Falquet
- Enseignant·e: Ivan Dario Mateus Gonzalez
- Enseignant·e: Jeferyd Yepes García