Course outside EMBL-EBI

Organisation and utilisation of hologenomic datasets

This course will cover the generation and application of large-scale holo-omic data sets, such as those produced within the HoloFood project.

There is an increasing recognition that organisms do not exist in isolation, but are actually holobionts, composed of the host and the many microorganisms found on or in the individual. The HoloFood project has developed significant multi-omics datasets for both chicken and salmon, with a view to understanding how different feeds impact the gut microbiota, and in turn animal productivity. This course covers how to access and utilise both raw and derived data products, the workflow to achieve genome-resolved metagenomics, analysis of host variation, generation and interpretation of metabolomic data, and approaches to multi-omic integration to understand links between traits and genomic information.

The HoloFood project represents a cornerstone of hologenomic research, providing a blueprint for how data from such projects should be archived, analysed and interlinked. As such, the motivation for this course is to highlight the availability and usability of the HoloFood data in further holo-omic analyses, either as reference sets to compare against, or as source data for subsequent novel analysis.

Participants will be required to provide their own wi-fi enabled laptops, with an up-to-date browser (e.g. Chrome v.98 or higher), and the ability to install cloud-client software (approx 2GB space required) to allow connection to the virtual machines that will be used for the course. Specifics of all technical requirements will be communicated prior to the course.

The training course is running as a precursor to the Applied HoloGenomics Conference (13 -15 September), also in Bilbao, Spain.

The course is organised by the HoloFood Innovation Action and has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 817729.

Who is this course for?

This course is aimed at researchers who are interested in generating their own, or utilising existing hologenomics datasets (such as HoloFood data). Ideal applicants should have experience working with large-scale data/systems biology, or have an anticipated project requiring access to or analysis of large-scale holo-omic data. Applicants are expected to be comfortable working in a Linux/command line environment.

What will I learn?

Learning outcomes

After the course you should be able to: 

  • Describe the HoloFood data that is available and how it was generated
  • Access a range of data types from leading public repositories
  • Illustrate how the data sets relate to each other
  • Use the data to support your own analysis  

Course content

During this course you will learn about: 

  • Omic data repositories: MGnify, European Nucleotide Archive, MetaboLights, BioSamples
  • Available HoloFood datasets: Genomic, Metagenomic, Metatranscriptomic, Metabolomic, Microbial Genome Catalogues
  • Analysis techniques: Metagenome assembly, recovery of genomes, functional annotation of genomes, environmental metabolomic analysis
  • Integration: Approaches and tools for further holo-omic analysis: e.g. integration of metabolomic data with (meta-)genomic data 


Germana Baldi
Jaelle Brearley
Robert Finn

Shyam Gopalakrishnan
Martin Hansen
Varsha Kale
Morten Limborg
Melanie Parejo
Jakob Rasmussen
Lorna Richardson
Alexander Rogers

This course has ended

11 - 12 September 2022
Villa De Bilbao
Charlotte Pearton

  • Robert Finn
  • Anna Fotaki
  • Lorna Richardson

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