Microbial Genomics Bioinformatician - Pipelines & Annotations

EMBL-EBI - European Bioinformatics Institute; Hinxton; On-site; GBP 35,000 - 42,000; Full time

Job summary

EMBL-EBI - European Bioinformatics Institute in Hinxton, United Kingdom is seeking a Bioinformatician to maintain Ensembl Microbes genomes, load new annotations, and ensure data accuracy. You will coordinate releases within a release-based environment and collaborate with Ensembl subteams and external partners.

The role requires strong Python, experience with workflows such as Nextflow or Snakemake, and familiarity with MySQL/PostgreSQL, UNIX/Linux, and HPC.

Qualifications

• PhD in bioinformatics, biology, computer science or related field, or MSc with equivalent professional experience.
• Knowledge of prokaryotic and/or microbial eukaryotic biology.
• Strong Python skills and production-quality code writing/understanding.
• Experience building computational pipelines with Nextflow, Snakemake or similar.
• Experience with relational databases (e.g. MySQL, PostgreSQL), UNIX/Linux, and HPC or cloud environments.
• Experience applying genome analysis/annotation tools and working with FASTA, GFF3 formats.
• Experience with software development best practices, including version control (Git), testing and code review.
• Familiarity with AI-assisted coding tools and evaluation of outputs.
• Excellent English communication skills, both written and spoken.
• Strong attention to detail and reproducible work.
• Ability to work independently and in a team.

Responsibilities

• Maintain the microbial genomes in Ensembl, including loading new genome annotations and ensuring data accuracy.
• Coordinate releases within a release-based environment with Ensembl subteams.
• Identify and assess genome annotation tools for microbial taxa beyond default annotations.
• Contribute to development of functional annotation pipelines and representation of microbial functions in Ensembl.
• Contribute to approaches for representing microbial pangenomes in Ensembl.
• Design, build and test technical solutions to improve processes.
• Create and maintain up-to-date documentation.
• Participate in code reviews and team meetings.
• Collaborate with EMBL-EBI groups and external collaborators, data generators and user communities.

Skills

Python

Nextflow

Snakemake

MySQL/PostgreSQL

UNIX/Linux

HPC/Cloud

FASTA/GFF3

Git

AI-assisted coding tools

English communication

Attention to detail

Independent & team work

Education

PhD in bioinformatics, biology, computer science or related field; or MSc with equivalent experience

Tools

Git

Job description

EMBL-EBI - European Bioinformatics Institute in Hinxton, United Kingdom is seeking a Bioinformatician to maintain Ensembl Microbes genomes, load new annotations, and ensure data accuracy. You will coordinate releases within a release-based environment and collaborate with Ensembl subteams and external partners.

The role requires strong Python, experience with workflows such as Nextflow or Snakemake, and familiarity with MySQL/PostgreSQL, UNIX/Linux, and HPC.