Metagenomics Course

Course Description

Next-generation sequencing (NGS) technologies have revolutionized many fields in biology and are changing the practice of medicine. One of the fields that have been particularly impacted is Metagenomics, which is the study of genetic material recovered directly from environmental samples without first culturing and isolating the organisms. Metagenomics analysis is used to explore the diversity, function, and ecology of different microbial communities such as microflora, water, soil, etc.

As a joint state-of-the-art research and training facility of the ETH and the University of Zurich, the Functional Genomics Center Zurich (FGCZ) offers a five-day course with hands-on practicals. The aim is to help scientists interested in NGS technologies, particularly applied to metagenome analysis tools, to gain a better understanding of the techniques available and their applications. 

The practical consists of a library preparation starting from genomic DNA, followed by a sequencing run on both, a bench top and a single molecule sequencer. An introduction to existing and upcoming NGS technologies is also provided.  Downstream analyses of the resulting data from both pipelines starts with the quality control and the management of the sequence data and expands to appropriate bioinformatics workflows to answer some of the key questions arising from this type of experiments (e.g., marker-gene and shotgun metagenomics).

The topics that will be covered include, methods of taxonomic assignment and clustering of targeted gene data; assembly, functional classification and characterization of shotgun metagenomic data; statistical models for estimating microbial diversity; and microbial community comparison methodology and metrics. 

The hands-on sessions for data analysis does neither require a pre-existing knowledge of Unix nor the command line environment. This course is not intended to be a training course for those solely interested in next-generation sequencing bioinformatics. This course is not meant to replace any manufacturers’ training normally supplied with an instrument.

By the end of the course participants should be able to design appropriate microbiome-focused experiments and make informed decisions about metagenomics-specific issues such as calling taxa, functional annotation, metagenome assembly and comparative metagenomics. Additionally, participants should be able to assess the advantages and limitations of metagenomic data analysis.

Course Programme

Library Prep

• DNA library generation: principles and types

Sequencing

• Detailed description of available sequencing technologies platforms
• Hands-on laboratory work: preparing and performing sequencing runs

Data analysis

• Overview of existing method for metagenomics data analysis
• Run QC: run assessment
• Read QC: metrics for read quality evaluation
• Preprocessing of the raw data
• Mapping reads to a reference database
• Examination of the community composition (taxonomic and functional)
• Evaluation of the community saturation and diversity
• Comparative analysis between samples
• Comparison of the results between platforms

Didactical approach

The course is conceived as highly interactive which includes:

• Theoretical inputs (lectures)
• Interactive discussions on case studies (group discussions)
• Pair and group work in the laboratory
• Instrument handling for the practical part
• Hands-on activities for data analysis (computer sessions)
• Q&A sessions, feedback and discussions with other participants and instructors
• Flash presentations by means of whiteboards or slides

Learning outcomes

At the end of the course, participants will be able to:
1. Demonstrate an understanding of NGS technologies;
2. Assess the challenges involved in investigating the metagenome;
3. Perform library preparation and sequencing procedures in the laboratory;
4. Assess the quality of the library as well as the data obtained
5. Perform basic data analysis using the Sushi pipeline and online available softwares
6. Apply NGS into a research-based context by:
a. formulating a meaningful research question
b. designing an experimental setup (based on the analytical techniques learned during the course) to address this specific question on metagenomics
c. presenting their strategy to the class

Important facts and how to apply

Target audience and prerequisites

The course is designed for established investigators, postdoctoral fellows and advanced graduate students from diverse biological fields.

Cost

The course tuition fees for PhD students from the University of Zürich and ETHZ is CHF 300.00 (Swiss francs) per person.  The price for postgraduate members of the University of Zürich or ETHZ is CHF 500.00.  Please note, that these prices can only be applied if the tuition fee is paid through an internal, i.e. University of Zürich or ETHZ, account.

For all other academics (paying through a non-UZH and non-ETHZ account) the cost is CHF 1,200.00 per person. For industrial delegates the cost for the course is CHF 1,500.00.

An invoice will be issued upon registration. This invoice will be sent out by email as well as a hard copy by regular mail/post. Those participants that register will be sent an email reserving their place together with an ‘Application Form’ to be signed by their correspondent supervisor and emailed back to the FGCZ. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed. 

IMPORTANT: The internal prices can be applied only, when paid by internal account.

Those participants that register will be sent an email reserving their place together with an ‘Application Form’ to be signed by their correspondent supervisor and emailed back to the FGCZ. Upon receiving the signed ‘Application Form’, the participant will be considered and their place in the course will be confirmed. An invoice will be issued. Please check our invoicing conditions before registering, see Question 13): FAQ Courses – Functional Genomics Center Zurich.  

Cancellation policy

Please note that due to the high demand for this course any change related to your participation should be informed as soon as possible, but not later than ten (10) working days (for internal participants) prior to the course start date if the invoice has not yet been issued. 20 working days for external participants.The cancellation request must be e-mailed to . If the cancellation of the course occurs after this time period, the tuition fee will not be refunded.

Please do not hesitate to contact us should you need any additional information or encounter any problems.