Software Engineer (Computational/Bioinformatics Pipelines)
Computational & Bioinformatics Pipeline Development
Sep 2022 - Present
At NatureMetrics, I work in the Bioinformatics Infrastructure Team, developing and maintaining computational/data pipelines for metabarcoding and metagenomic data, across multiple sequencing platforms for global biodiversity analysis services (eDNA sampling kits).
Pipeline development was predominantly using NextFlow, BASH, Python both on-prem. and on AWS.
- Primary focus is on scalable computation i.e. bioinformatics data pipelines for commercial product delivery, i.e working with lead bioinformatician (R&D) to productionise applications and code in a high-throughput, scalable environment.
- Development and maintainance of databases for pipelines (Postgres, MySQL)
- Migration of computational pipelines to AWS, including their DBs (Postgres)
- Work done in an agile manner and environment, adopting best-practices where practical.
- Testing & benchmarking of pipelines
- Maintain testing frameworks, CI/CD and own the process of moving from test to production environments.
- Support the strategic development of Bioinformatics infrastructure.
- Documentation of Bioinformatics pipeline development & deployment.