Shotgun metagenomics, the non-targeted sequencing of genomes from all microorganisms in a sample, has brought new insights into microbial ecology. However, the limited length of individual metagenomic reads (far smaller than individual genes) is limiting downstream analyses, stressing the need to reconstruct reads and make sense of this output. On this front, genome-resolved metagenomics has emerged as a highly effective way to identify genomes directly from the metagenomic assembly outputs, bypassing cultivation to explore the gene content of individual microbial populations. With the ever-increasing use of applying next generation sequencing technologies to an array of environmental samples (e.g., microbiomes, oceans, soils), genome-resolved metagenomics has gained increased attention. Reconstructing and analysing genomes using metagenomic data as a starting point can be incredibly informative, but requires the understanding of key biological concepts (e.g., what is a bacterial population) and learning of bioinformatics tools (e.g., how to handle metagenomic assemblies and curate individual genomes).
This course will cover both the biological concepts and bioinformatics tools to take best advantage of the rapidly growing field of genome-resolved metagenomics. Participants will also briefly be introduced to the analysis of micro-diversity through single-nucleotide variants and processing of pangenomes to take best advantage of newly characterised genomes. Course material will be based on a mixture of lectures and hands-on exercises with real datasets for participants to practice on. The course is intended for researchers and graduate students who plan on studying microorganisms with metagenomics, and are especially interested in genomics through genome-resolved metagenomics.
Participants should expect to gather a good understanding of genome-resolved metagenomics, which they will be able to apply to their own metagenomic datasets.
Graduate or postgraduate degree in Biology, Life or Earth Sciences, familiarity with the UNIX terminal environment. Participants must have a personal computer (Windows, Mac, Linux) and access to a good internet connection. The use of a webcam and headphones is strongly recommended.
Participants are expected to have anvi’o installed in their own computer ahead of the start of the course (http://merenlab.org/2016/06/26/installation-v2), but support for troubleshooting will be provided ahead of the course. Ideally, participants should already have generated or are in the process of generating their own metagenomic datasets that will require the analysis mentioned in this workshop. However, this is not required, since reference data will be shared with all participants to perform the exercises.
A good internet connection is required to follow the course.
Thursday, February 4th (optional 1hr session)
Installation of anvi’o – troubleshooting
Monday, February 8th
Introduction to biological concepts
Introduction to bioinformatics tools
Tuesday, February 9th
Introduction to the anvi’o interface
Wednesday, February 10th
Thursday, February 11th
Extracting genomes from TARA Oceans
Friday, February 12th
Open discussions on special topics linked to the participants’ interests
Summary of the week
- Course Fee
- Early bird (until December 31st, 2020):
- 440 € *
(352 € for Ambassador Institutions)
- Regular (after December 31st, 2020):
- 575 € *
(460 € for Ambassador Institutions)
- Prices are VAT included.
* Participants from companies/industry will have an extra charge of 100 €.