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Scientific Programmer - Nanopore

Job Location
Wellcome Genome Campus
CB10 1SD
United Kingdom
Job Description

The European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) is seeking a Scientific Programmer to join the European Variation Archive (EVA) and European Genome-phenome Archive (EGA) team led by Thomas Keane. The main purpose of the role is to work on a collaboration between EMBL-EBI, Oxford Nanopore Technologies, and the Global Alliance for Genomics and Health (GA4GH) to enable the use of GA4GH standards with nanopore sequencing data.

Oxford Nanopore develop third generation sequencing technologies that use biological pores and electronic sensors to sequence long fragments of DNA. The platform is now entering production at thousands of sites around the world, and the volume of sequencing data and number of sequencing experiments that use nanopore technology is set to increase dramatically. The GA4GH is an organisation that develops genome data standards to enable international interoperability to accelerate the potential of genomics research to advance human health. The EGA and EVA are active contributors to GA4GH and have implemented many GA4GH standards for data sharing. The CRAM format is a highly compressed standard for storing and accessing DNA sequencing data with widespread adoption amongst genome data tools, pipelines, sequencing platforms, and software libraries.

We are a diverse team from around the globe that come from interdisciplinary backgrounds including biology, computing, physics, mathematics, and business. We work in a highly collaborative environment where new and innovative ideas are the cornerstone for success. We welcome individuals with little domain knowledge and provide the opportunity to gain hands-on experience at working on a project with major scientific impact in a world-leading bioinformatics institute. Our aim is to enable our team members to reach their personal and professional goals in a happy and engaging working environment.  Your roleIn this role, you will be responsible for developing methods and tools for optimal compression, conversion, and exchange of ONT data in GA4GH standards such as the CRAM format  ( and htsget data streaming API ( You will collaborate with the Large Scale Genomics workstream of GA4GH and with nanopore sequencing experts in the community. You will evaluate alternative compression strategies and benchmark implementations, and promote the use of GA4GH formats for exchange of nanopore sequencing data.  You haveThe ideal candidate will hold a higher degree in a technical discipline such as Engineering, Computing, or Bioinformatics. An additional degree qualification and knowledge of genomics would be advantageous. In addition, the successful candidate must have the following skills:

  • Proven experience in collaborative software development projects
  • Minimum 3 years experience in scientific software development
  • Thorough and organised. You can follow up where results diverge from expectations, and assess and address those difference
  • Good communication and interpersonal skills, both oral and written
  • Ability to work to tight deadlines
  • Ability to interpret and contribute to technical documents
  • Familiarity with working in unix environments
  • Proficiency in written and spoken English

 You might also have

  • Experience with source control systems and testing frameworks
  • Experience working within an agile framework
  • Knowledge of genomics or related scientific area
  • Experience developing and maintaining scientific software
  • Scripting languages frequently used in bioinformatics such as Python, Perl or R

Why join usAt EMBL-EBI, we help scientists realise the potential of ‘big data’ in biology by enabling them to exploit complex information to make discoveries that benefit mankind. Working for EMBL-EBI gives you an opportunity to apply your skills and energy for the greater good. As part of the European Molecular Biology Laboratory (EMBL), we are a non-profit, intergovernmental organisation funded by over 27 member states and two associate member states. We are located on the Wellcome Genome Campus near Cambridge in the UK, and our 850 staff are engineers, technicians, scientists and other professionals from all over the world.

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organisation. The remuneration package comprises a competitive salary, a comprehensive pension scheme and health insurance, educational and other family related benefits where applicable, as well as financial support for relocation and installation. For more information about pay and benefits please visit our website. 

We have an informal culture, international working environment and excellent professional development opportunities but one of the really amazing things about us is the concentration of technical and scientific expertise – something you probably won’t find anywhere else.

If you’ve ever visited the campus you’ll have experienced first-hand our friendly, collegial and supportive atmosphere, set in the beautiful Cambridgeshire countryside. Our staff also enjoy excellent sports facilities including a gym, a free shuttle bus, an on-site nursery, cafés and restaurant and a library.What else you need to knowTo view a copy of the full job description please visit our website.

To apply please submit a covering letter and CV through our online system. Applications are welcome from all nationalities and this will continue after Brexit. For more information please see our website. Visa information will be discussed in more depth with applicants selected for interview.

EMBL-EBI is committed to achieving gender balance and strongly encourages applications from women, who are currently under-represented at all levels.

Appointment will be based on merit alone.

This position is limited to the project duration specified.

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