This course will cover the entire arc of a reference genome project; from sample acquisition and shipping, through nucleic acid extraction, sequencing, assembly, curation and annotation in public databases. It will promote the use and reuse of aquatic genomic data, build a community of researchers able to exploit these new data types, and introduce them to the theory and practice of reference quality genome sequencing and assembly. The course content will connect participants to researchers at the forefront of the biodiversity genomics revolution and meet with others worldwide who also aim to apply these new approaches to their study systems.

Participants will develop bioinformatics skills to quality assess raw genomic sequence data, identify co-bionts, assemble data into a genome build, assess and then annotate the model with biological significance.

Symbiosis lies at the heart of the origins of the eukaryotic cell, and new symbiosis events today shape much of the natural world, playing key roles in ecosystem engineering and in colonisation of extreme habitats such as hydrothermal vents. Biological understanding of symbiosis will be hugely enhanced through the deep analysis of the genomes of the interacting partners, and the Aquatic Symbiosis Genomics project is working globally to generate reference genomes for many symbints from marine and freshwater habitats.

Virtual course

Participants will learn via a mix of lectures, technical presentations, group work, and discussion sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and communication via Slack.

Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.

Participants will need to be available between the hours of 09:45-17:30 GMT each day of the course. Trainers will be available to assist, answer questions and further explain the analysis during these times.

Who is this course for?

The course is aimed at early-stage researchers working in the field of ecological genomics who want to make bioinformatics a significant part of their research. The course will also support the research of the Moore Foundation symbiosis community, in particular those working on the Aquatic Symbiosis Genomes project.

Participants will require a basic knowledge of the Unix command line and the Ubuntu 18 operating system. We recommend taking these tutorials:

• Basic introduction to the Unix environment:
  • www.ee.surrey.ac.uk/Teaching/Unix
• Introduction and exercises for Linux:
  • https://training.linuxfoundation.org/free-linux-training

Experience with both R and Python will also be essential for the computational sessions. Participants without basic knowledge of these resources will struggle to learn the practical skills developed during the course.

What will I learn?

Learning outcomes

After this course you should be able to:

• Devise effective strategies for nucleic acid extraction, sequencing, assembly and annotation for their species of interest
• Assess raw and analysed genome sequence data in a critical manner
• Implement advanced assembly and annotation approaches in building and interrogating genomes
• Integrate wet-lab, sequencing and bioinformatics technologies to assemble high-quality genomes
• Participate in building a community of practice to support further research

Course content

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form providing answers as directed
• Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography
  • work history
  • current research interests
• Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by midnight on Friday 16 July 2021. 

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Monday 9 August 2021. If you have any questions regarding the application process please contact Lucie Smith (lsmith@ebi.ac.uk).