Bioinformatics Developer Ensembl Comparative Genomics EMBL-EBI - European Bioinformatics Instit[...]

EMBL EBI; Saffron Walden; On-site; GBP 35,000 - 50,000; Full time

Job summary

A leading genomics organization in Saffron Walden is seeking a motivated bioinformatician to develop and maintain Comparative Genomics pipelines. The candidate should possess a Master/PhD background in bioinformatics or related fields with strong skills in comparative genomics and programming (Python). Responsibilities include assisting in technical decisions, supporting users, and participating in collaborations across global biodiversity initiatives. This role offers the opportunity to contribute to world-class genomic data resources.

Qualifications

• Strong knowledge of whole-genome alignment and gene/species-tree reconstruction.
• Experience in managing genomics data with proficiency in command-line tools.
• Hands-on experience with Workflow systems for large-scale datasets.

Responsibilities

• Maintain and develop Ensembl Comparative Genomics pipelines.
• Assist project leader in technical decisions.
• Support external users in utilizing genomic data resources.

Skills

Comparative genomics

Python

UNIX/Linux

SQL

Nextflow/Snakemake

Machine learning

MongoDB

GraphQL APIs

Education

Master/PhD in bioinformatics, molecular biology, data sciences

Tools

Docker

Version control

Job description

Your primary tasks will be to maintain, run and develop our Comparative Genomics pipelines. This will include working closely with collaborators and gaining in-depth knowledge of gene and species tree inference, multiple genome alignment, workflow managers and Python-based technologies.,

• Maintaining, running, and developing the Ensembl Comparative Genomics pipelines, databases and API;
• Assisting the project leader in making technical decisions for the project;
• Helping with the coordination of the Ensembl comparative genomics release process;
• Supporting external users in their use of the comparative genomics pipelines;
• Applying scientific expertise to advance resource development;
• Participation in collaborations between Ensembl and other research groups and scientific consortia and representing the project and the institute at conferences.

• Master/PhD in bioinformatics or molecular biology, bioinformatics, data sciences or a related field (or equivalent practical experience);
• Strong knowledge of comparative genomics, including whole-genome alignment, gene and species-tree reconstruction, sources of bias/error and associated software and tools;
• Experience in bioinformatics and the management of genomics data;
• Proficiency in at least one programming language (e.g., Python);
• Proficiency working in a UNIX/Linux environment, using command-line tools and version control;
• Proficiency with relational databases and SQL;
• Hands-on experience with Workflow systems Nextflow/Snakemake, or similar;
• Excellent organisational and communication skills;
• Experience working on high-performance clusters and cloud computing;
• Experience with Singularity/Docker to run containers on a shared compute environment;
• Working within a release cycle for software or data;
• Experience with MongoDB and building GraphQL APIs;
• Experience in driving and leading software projects;
• Working knowledge of machine learning concepts;
• Experience working on scientific projects in the field of comparative genome analysis.

We are seeking a highly motivated and experienced bioinformatician to help expand the Comparative Genomics resources in Ensembl, a world-leading provider of genomics data, infrastructure, and tools.

There are a growing number of global biodiversity initiatives, such as Darwin Tree of Life, the Vertebrate Genomes Project, the European Reference Genome Atlas and the Human pangenome reference graph consortium, providing high-quality reference genomes and pangenomes for eukaryotic species. Ensembl provides a platform for the annotation and comparison of these genomes, from the single-species pangenome level right up to annotating and modelling the evolutionary relationships across all eukaryotes. You will join the Ensembl Comparative Genomics team, whose work spans computational biology, software development, large-scale computing, big data, workflow management and automation. The Comparative Genomics team provides resources to help researchers understand the relationships between species. The team generates data on orthologues, gene trees, large scale syntenies, whole genome alignments and a variety of other analyses. A primary objective is to ensure these analyses remain scalable with the growing influx of high-quality genomes being added each year. As part of the Comparative Genomics team you will work with the Eukaryotic Annotation team and several other teams in the Ensembl project, as well as research consortia and communities from across the globe. On joining the team, you will play a key role in developing software and workflows to compare thousands of genomes, directly contributing to making Ensembl a world leading resource for the comparative analysis of genomic diversity.