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.

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