Bioinformatics Software Engineer at Dakota Consulting

Palo Alto, CA 94301

About the Job

Dakota Consulting, Inc. is a growing company that provides innovative business, IT, scientific research, and cybersecurity services to Federal and commercial customers. Dakota’s objective is to provide services that meets customers’ needs and exceeds their expectations. Our core values include honesty; a commitment to exceptional customer service; and providing a respectful, fun, challenging, and learning place of employment. We actively recruit for dedicated technically competent individuals and partners that are self-motivated while performing exceptionally well in a collaborative team effort. Dakota’s headquarters are in Silver Spring, MD.

Dakota is seeking a candidate to provide support to our federal customer to contribute in working with the stakeholder community (federal, state and academic) through the Genome in a Bottle Consortium and the Joint Initiative for Metrology in Biology to develop reference materials, reference data, and reference methods for genome sequencing.  The work includes software engineering of bioinformatics analyses of human whole genome sequencing data.  Suitable candidate must be able to assist in software engineering of bioinformatics methods to analyze genome sequencing data for reference materials.

Job Functions
  1. Engineer the Genome in a Bottle small variant integration pipeline to enable efficient use on any genome. 
  2. Work with Genome in a Bottle stakeholders to understand requirements for tools development to enhance workflow efficiency and robustness
  3. Develop a dashboard for stratified small variant performance metrics.  The Global Alliance for Genomics and Health Benchmarking Task Team has developed methods to benchmark variant calling, but further development is needed to prioritize display of statistics. 
  4. Develop a pipeline for generating candidate calls for difficult variants such as large indels and structural variants from multiple technologies.
Experience Requirements

Two or more years’ experience in bioinformatics or computational biology

Skills and Abilities
  • Proficiency in at least one general-purpose programming language: Python, Java, C++, etc
  • Proficiency in a scientific data processing ecosystem: R, Python/Numpy, etc
  • Experience with Linux required
  • Experience with high-performance parallel computing clusters or cloud environments
  • Good understanding of software best practices, agile methodologies and/or software architecture
  • Experience with software engineering best practices: code quality, testing, performance optimization, development of research tools infrastructure
  • Ability to describe technical information in simple, clear language.
  • Excellent customer care skills and abilities – key effective verbal, written, and listening communication skills
  • Ability to work independently as well as with other team members.

Bachelor’s Degree in Computer Science, Biological Sciences, or Physical Sciences, preferably related to computational biology


Must be able to obtain a Public Trust clearance

Dakota Consulting, Inc. is an Equal Opportunity Employer. AA/M/F/Vet/Disability

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