This workshop will introduce cloud technologies for creating bioinformatics pipelines relevant to clinical decision making. The content will guide participants through the process of building data flows, using GA4GH standards and infrastructure available from ELIXIR nodes and the EMBL-EBI. Expertise and support will be available during the workshop from the trainers, allowing participants to tailor pipelines to suit their own needs, data types and analysis methods.

The workshop content will cover aspects of data storage and collection with regards to standards and file formats; sharing data and metadata within the cloud community; visualisation and analysis of data with regards to end-point clinical decision making.   

Who is this course for?

This workshop is aimed at bioinformaticians, software engineers and data analysts working in genomic medicine. Participants are likely to be working to set up and operate compute infrastructure and analysis pipeline to support clinical decision making in genomic medicine.

Participants will require a basic knowledge of computational script writing and command line tools. Knowledge of next generation sequencing technologies and familiarity with genomic data will be useful for comprehending the content.

What will I learn?

Learning outcomes

After this course you should be able to:

• Store patient genomic data and metadata
• Run a Variant Calling Pipeline using a client/server model for data transfer
• Make genomic data and metadata discoverable by external users
• Enable external users to send selected workflows to analyse data
• Apply approaches and software solutions for variant annotation and interpretation

Course content

During this workshop you will learn about:

• GA4GH data standards including:
  • htsget API, CRAM, VCF, Beacon API, Data Use Ontology
• Tools to assist clinical decision making:
  • VEP, PanelApp, IGV  

Trainers

In order to be considered for a place on this course, you must do the following:

• Complete the online application form in as much detail as possible
• Please submit the application online by 23:00 CET on Friday 5 June 2020

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by Friday 12 June 2020. The organisers will attempt to review applications as and when they are submitted, and will contact successful participants as early as possible. If you require a visa to travel to Denmark please submit your application as soon as possible to allow time to apply for the necessary documentation.

Applicants need to arrange own travel and accommodation for this event. 

The workshop includes lunch and refreshments.