Metagenome-atlas: Three commands to start analysing your metagenome data

Please be aware that to comply with recent federal and cantonal recommendations, you will most probably have the obligation to present a COVID certificate to be able to attend the course. Take this into consideration before applying to this course.

Overview

Metagenomics transformed how we study microbiomes by enabling the analysis of entire microbial communities from diverse environments, without the need for culturing. Recent improvements in algorithms enabled the assembly of larger and larger contigs from metagenomes, which then can be clustered together to produce draft genomes of new species. In this way, an almost unimaginable number of genomes from uncultured microbes could be assembled. These genomes allow for dataset-specific taxonomic analysis and genome-resolved functional annotation of metagenomes.

In this course, we will familiarize the participants with the steps required in assembly-based metagenomics (assembly, binning, genome completeness estimation, taxonomic and functional annotation). In the hand-on session we will use metagenome-atlas, a pipeline which implements the most commonly used metagenomics tools in a single workflow allowing users to get started in three commands analyzing your metagenome data. Finally, we will show how to use the output of metagenome-atlas to answer scientific questions.

Audience

PhD students, postdocs and other researchers, from any scientific environment (academia, facilities, companies, etc.) interested in analysing metagenomics data with Metagenome-Atlas.

Learning outcomes

At the end of the course, the participants will be able to:

• Describe the advantages and challenges of assembly-based metagenomics
• Assemble genomes from metagenomic reads and estimate their quality
• Quantify genomes in a dataset
• Evaluate the results of the analyses

Prerequisites

Knowledge / competencies

To benefit optimally from the workshop, participants should have an understanding of microbiome sequence analysis, e.g., already have worked with 16S rDNA sequencing data. We recommend the course "Understanding 16S rDNA sequencing" if this prerequisite is not met.

The participants should know what a fastq file is and how to run commands in bash. The participants should have some familiarity with R or Python, for instance be able to open a table in either of the languages.

Technical

For the hands-on-session we will provide a virtual environment with all software pre-installed. The participants should have a computer with a not-too old web browser. A wired connection to the internet improves the experience.

Application

The registration fees for academics are 60 CHF and 300 CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for free-of-charge cancellation is set to 23/11/2020. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

University of Lausanne (Metro M1 line, Sorge station). The course will start at 9:00 and end around 17:00. Precise information will be provided to the participants in due time.

Additional information

Coordination: Valeria Di Cola

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.