MGnify is EMBL-EBI’s microbiome sequence data analysis resource, which performs the archiving, assembly and analysis of amplicon, metagenomic and metatranscriptomic data. Alongside the large-scale analysis of existing public microbiome datasets in ENA, we are participants in several projects investigating various aspects of microbiome research. For example we are a partner in FindingPheno which aims to find drivers of phenotype in food production systems to unlock the full potential of microbiome interventions for health and sustainability in commercial food production. One aspect of this will be to improve our understanding of carbohydrate utilization in host-associated microbiomes.
The aims of these projects require support and expanded functionality of our existing pipelines, increased automation and scalability, and updated visualisations to accommodate new data products, tools, and applications.
This position will focus on data analysis, pipeline development, addition of further tools to the MGnify repertoire, and the propagation of new data products into the MGnify data store. It will also include analysis of other MGnify data products such as the protein sequence database to improve functional predictions.
Your Role
- Analysis and assembly of metagenomic and metatranscriptomic data produced within the projects and related public datasets
- Using genome-resolved methods to produce and update genome catalogues for prokaryotes, eukaryotes and viruses
- Using a range of methods and tools to conduct specific analyses on the MGnify platform such as homology searches, genomic context, protein analysis and functional predictions
- Evaluate existing and new tools and methods in the field
- Optimising bioinformatic pipelines
- Respond to user and project consortia queries
- Attend regular project meetings as required, to enable consistent and clear communication to and from the microbiome informatics team
- Interact with teams at EMBL-EBI, to allow appropriate data to be extracted from their resources (e.g., API) and/or submitted to relevant resources
You Have
Masters level or equivalent qualification/experience in computational, biological or related scientific discipline.
The ideal candidate would have worked within a professional environment for two or more years, running microbiome analysis pipelines and contributing to their development.
- Strong scripting skills in Python and R
- Workflow languages (e.g. Common Workflow Language, Nextflow or SnakeMake)
- Knowledge of metagenomics analysis and tools
- Knowledge of protein functional annotation systems
- Use of compute cluster job schedulers (e.g. Slurm)
- Experience using Git/Github
- Experience running and maintaining bioinformatics pipelines
- Examples of independent data analysis
- Unix/Linux experience
The candidate will need to be able to work independently, as well as interact with the rest of the development team, and other members of the project consortia. Good communication skills and attention to detail are essential, as is the ability to work to deadlines and solve problems when they arise. The successful candidate will be expected to bridge between microbiome informatics team and the wider project consortia. This will be achieved via regular meetings and videoconferencing. The primary direction for the pipeline development and data analysis will come from the team leader and line manager. Other requirements may also come from other team members and the consortia. The postholder will also be required to interact with members of other teams at EMBL-EBI.
You might also have
- Software development in a production environment
- Relational database skills including querying, basic schema design and optimization
- Experience of working with protein structural model predictions
- Working experience with profile HMMs
- Experience deploying pipelines in a distributed environment, ideally using a commercial cloud platform
Why join us
Do something meaningful
At EMBL-EBIyou 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 theWellcome 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.
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
- 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 (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 more details please see our employee benefits page.
What Else You Need To Know
- Contract duration: This position is a 1 year project based contract.
- 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.
- EMBL is a signatory of DORA. Find out how we implement best practices in research assessment in our recruitment processes here.
- 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.
- How to apply: To apply please submit a cover letter and a CV through our online system.
