Location:	EMBL-EBI, Hinxton near Cambridge, UK
Contract Duration:	2 years (project position)
Salary:	Grade 5.0 Monthly salary starting at £3.303 after tax but excluding pension and insurance contributions. Plus generous benefits.
Closing Date:	11/12/2025
Reference Number:	JR2615

The Ensembl Genebuild team at EMBL-EBI develops high-throughput, high-quality genome annotation pipelines that underpin our mission to provide comprehensive, open-access genomic data resources. Our work spans the eukaryotic tree of life, contributing to global biodiversity initiatives. These ambitious efforts aim to sequence, assemble, and annotate genomes from tens of thousands of species, generating foundational data for conservation, evolution, and functional biology.

To support this, we are building a new, modular genome annotation system optimised for scalability, reproducibility, and long-term sustainability. This work will enable the annotation of highly diverse species from invertebrates and protists to plants and vertebrates, each bringing unique biological challenges and opportunities.

Your role 

We are looking for a skilled, motivated bioinformatics developer to join our team and help develop the next generation of Ensembl genome annotation tools and infrastructure. In this role, you will:

• Design and implement scalable genome annotation workflows tailored for large-scale biodiversity projects.
• Develop robust, reproducible pipelines using workflow managers such as Nextflow.
• Modernise and re-engineer legacy tools into modular, maintainable components using current best practices.
• Integrate data from transcriptomics, proteomics, and comparative genomics to improve annotation quality across diverse taxa.
• Collaborate with international partners to standardise approaches and ensure interoperability across global efforts.

You have 

• Proficiency in Python and other relevant languages for bioinformatics tool development.
• Experience developing or maintaining bioinformatics pipelines using workflow management systems like Nextflow or Snakemake.
• Solid understanding of algorithm development and performance optimisation for large-scale data.
• Working knowledge of eukaryotic genome annotation, transcriptome analysis, or comparative genomics.
• Strong working knowledge of Linux command-line environments, version control (e.g., Git), and software testing for robust, reproducible workflows.
• Experience in high-performance computing and workflow optimisation, including cloud computing, cluster computing, or GPU-based acceleration.
• Excellent communication skills with a problem-solving mindset and the ability to work both independently and collaboratively with cross-functional teams.

You may also have

• Experience working on non-model or taxonomically diverse genomes.
• Familiarity with data models for gene annotation or genome feature representation.
• Knowledge of long-read transcriptomics (Iso-Seq, Nanopore).
• Contributions to open-source software projects or community genome resources.
• Experience mentoring or training others in bioinformatics methods, workflows, or best coding practices.
• Hand-on experience with containers particularly Docker and Singularity
• Experience in working with large relational databases 
• Experience working with GenAI or LLM applications

Contract length:

2 year project position

Salary:

Grade 5.0 Monthly salary starting at £3.303 after tax but excluding pension and insurance contributions. Plus generous benefits.

Interviews:

Shortlisted and invited candidates will be contacted via email for introductory calls from early January 2026.

Why join us

Do something meaningful
At EMBL-EBI you can apply your talent and passion to accelerate science and tackle some of humankind’s greatest challenges. EMBL-EBI, part of the European Molecular Biology Laboratory, is a worldwide leader in the storage, analysis and dissemination of large biological datasets. We provide the global research community with access to publicly available databases and tools which are crucial for the advancement of healthcare, food security, and biodiversity.
 

Join a culture of innovation
We are located on the Wellcome Genome Campus, alongside other prominent research and biotech organisations, and surrounded by beautiful Cambridgeshire countryside. This is a highly collaborative and inclusive community where our employees enjoy a relaxed atmosphere. We are committed to ensuring our employees feel valued, supported and empowered to reach their professional potential.  Watch this video to see how EMBL-EBI makes an impact.

Enjoy lots of benefits:

• Financial incentives: Monthly family, child and non-resident allowances, annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Flexible working arrangements – including hybrid working patterns 
• Private medical insurance for you and your immediate family (including all prescriptions and generous dental & optical cover)
• Generous time off: 30 days annual leave per year, in addition public holidays
• Relocation package including installation grant (if required)
• Campus life: Free shuttle bus to and from work, on-site library, subsidised on-site gym and cafeteria, casual dress code, extensive sports and social club activities (on campus and remotely)
• Family benefits: On-site nursery, 10 days of child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Benefits for non-UK residents: Visa exemption, education grant for private schooling, financial support to travel back to your home country every second year and a monthly non-resident allowance.

For detailed information please visit our employee benefits page here. 

What else you need to know

• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Please take a look at our International Applicants page for further information.  
• EMBL is a signatory of DORA. Find out how we apply DORA principles to our recruitment and performance assessment processes here.
• Diversity and inclusion: At EMBL, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ & individuals from all nationalities. 
• How to apply: To apply please submit a cover letter and a CV through our online system. Applications will close at 23:59 CET on the date shown below. We aim to provide a response within two weeks after the closing date.

Closing Date

11/12/2025