Bioinformatics Engineer Job at Theery, South San Francisco, CA

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  • Theery
  • South San Francisco, CA

Job Description

As a Bioinformatics Pipeline Engineer, you will be responsible for the design, development, and maintenance of bioinformatics pipelines, primarily using Oxford Nanopore reads. You will collaborate with the bioinformatic and wet lab scientists to understand and implement the specific pipeline goals, while applying your software engineering expertise. A primary focus will be ensuring that our pipelines are robust, scalable, and meet high coding standards.

In this job you will:

  • Develop and maintain bioinformatics pipelines using Snakemake.
  • Optimize existing pipelines for performance, reliability, scalability, and maintainability using best practices.
  • Troubleshoot and resolve issues in pipelines, including handling edge cases related to biological and sequencing artifacts.
  • Collaborate with both scientists and engineers.
  • Provide support and training to the tech support team on pipeline usage and troubleshooting.
  • Explore and integrate new bioinformatics tools and technologies to improve pipelines.

Requirements

  • 4+ years of experience developing level production bioinformatics pipelines using Snakemake or NextFlow.
  • Experience in Oxford Nanopore reads.
  • Illumina sequencing.

Tech stack:

Snakemake, Nextflow, Python, Conda, Docker / Apptainer / Singularity, AWS (lambda, S3, RDS), Git + Github Actions.

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