Bioinformatics Software Developer

2 months ago

Oxford, Oxfordshire, United Kingdom Oxford Nanopore Technologies Full time

Oxford Nanopore Technologies is headquartered at the Oxford Science Park outside Oxford, UK, with satellite offices and commercial presence in many global locations across the US, APAC and Europe. Oxford Nanopore employs from multiple subject areas including nanopore science, molecular biology and applications, informatics, engineering, electronics, manufacturing and commercialisation. The management team, led by CEO Dr Gordon Sanghera, has a track record of delivering disruptive technologies to the market.
Oxford Nanopore's sequencing platform is the only technology that offers real-time analysis (for rapid insights), in fully scalable formats from pocket to population scale, that can analyse native DNA or RNA and sequence any length of fragment to achieve short to ultra-long read lengths.
Our goal is to enable the analysis of any living thing, by anyone, anywhere. We offer real-time nanopore-based DNA/RNA sequencing technology: accessible, easy to use and fully scalable for any requirement.
The Role...
The Customer Analysis Workflows group at Oxford Nanopore Technologies' is responsible for communicating bioinformatic analyses to end users through various media from software libraries, notebook tutorials, through to fully automated analyses on the EPI2ME platform
The Details...
Reporting to the Associate Director Bioinformatics Software Development, the successful candidate will be driven to provide scientific analysis, software friendly to a range of user abilities. You will be responsible primarily for maintaining bioinformatic analyses to be coupled with particular experiment scenarios, targeting particular scientific and clinical questions. You will work with our team to test and deploy workflows that can be utilised across modes of presentation from standalone libraries and command line tools, to coordinated graphical solutions. Key responsibilities will be to:
- take ownership of our continuous integration and deployment systems for workflow development;
- adapt standard bioinformatic tools to long-read nanopore sequencing;
- seek out performance and useability improvements in core bioinformatic tools
- identify areas for tool development, and work with Algorithm Research colleagues to explore options;
- define new and innovative ways to test and deploy Nextflow workflows;
- define and promote best-practices for ONT's open-source analysis software;
- work with our cloud platform team to best deploy workflows in the cloud, and our instrument software team for deployment on sequencing devices
- maintain abreast of external advances in the field of long-read data analysis and the requirements of end-users as determined by various customer facing teams.
What We're Looking For...
You will hold at least a MSc (or equivalent experience) involving a meaningful amount of programming in a high-level language. A PhD or proven experience requiring understanding of DNA/RNA sequencing analysis is desirable. We would also like you to have:
- experience in software development on Debian-based linuxes;
- familiarity with continuous integration and deployment (particularly GitLab);
- expertise in bioinformatics workflows and knowledge of workflow management software (particularly Nextflow) and practical experience of handling sequencing data with exposure to common software (samtools, bcftools);
- familiarity with long-read sequencing;
- strong Python programming skills (development, testing, packaging);
- fluency in one or more of C, C++, or Rust;
- knowledge or docker, singularity, slurm, grid engine, and all things HPC
Please note that no terminology in this advert is intended to discriminate on the grounds of a person's gender, marital status, race, religion, colour, age, disability or sexual orientation.

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