Bioinformatics Developer

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 bioinformatic 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

Apply now! Benefits and Contract Information

• Financial incentives: depending on circumstances, monthly family/marriage allowance of £278 monthly child allowance of £336 per child. Non resident allowance up to £569 per month. Annual salary review, pension scheme, death benefit, long-term care, accident-at-work and unemployment insurances
• Hybrid working arrangements
• 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 to eight bank holidays
• Relocation package including installation grant (as applicable)
• 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, child sick leave, generous parental leave, holiday clubs on campus and monthly family and child allowances
• Contract duration: This position is a 2 year project based contract
• Salary: Monthly salary starting at £3,303 after tax but excl. pension & insurances) + benefits (Total package will be dependent on family circumstances) 
• International applicants: We recruit internationally and successful candidates are offered visa exemptions. Read more on our page for international applicants.
• Diversity and inclusion: At EMBL-EBI, we strongly believe that inclusive and diverse teams benefit from higher levels of innovation and creative thought. We encourage applications from women, LGBTQ+ and individuals from all nationalities.
• Job location: This role is based in Hinxton, near Cambridge, UK. You will be required to relocate if you are based overseas and you will receive a generous relocation package to support you.