BIOINFORMATICS PROGRAMMER JOB DESCRIPTION

A Bioinformatics Programmer who cannot keep variant calling pipelines current leaves research teams blind to the genetic mutations their studies depend on finding. Whole-genome and exome analysis demands someone who owns the full technical stack, from pipeline architecture on high-performance computing clusters to the web-based browsers that make aggregate data legible to scientists. This role sits within a research computing function that serves multiple laboratories simultaneously. Reproducibility and documentation are not afterthoughts here - they are the standard by which the work is judged.

As the Bioinformatics Programmer, you will design, implement, and maintain the sequencing data pipelines and visualization tools that enable gene discovery and clinical genomics research across multiple intramural laboratories. You will collaborate directly with sequencing center staff, research scientists, and computing infrastructure teams, operating within a research environment where pipeline accuracy and data reproducibility determine the validity of scientific outcomes.

Career Impact: Deep hands-on experience with GATK variant calling and next-generation sequencing data analysis builds the kind of domain credibility that is recognized across academic medical centers and government research institutions.

Business Impact: The pipelines and genome browsers you maintain determine whether research teams can identify disease-causing mutations at the pace their studies require.

Growth Opportunity: Gaining proficiency in structural variant detection, copy number analysis, and cloud-based genomics positions you for senior computational biology or bioinformatics engineering roles.

• Develop and maintain whole-genome and exome variant calling methodologies supporting gene discovery and clinical research projects.
• Implement omics data processing workflows in both local high-performance computing and cloud environments.
• Design and maintain web-based genome browsers for visualizing and querying aggregate sequencing data.
• Collaborate with sequencing center staff to evaluate and integrate data from emerging sequencing methodologies.
• Manage large omics dataset collections including data quality control and cloud import and export operations.
• Write well-documented code, conduct code reviews, and perform workflow benchmarking to maintain pipeline integrity.
• Prepare SOPs and project documentation to ensure all methodologies are reproducible and transferable.
• Train junior bioinformatics staff in pipeline development and optimization for supercomputing environments.

• Bachelor's degree in Bioinformatics, Computer Science, Genomics, or a related field, or equivalent work experience.
• Two or more years of post-degree bioinformatics experience, with demonstrated proficiency in variant calling pipeline execution and genotype data management.
• Proficiency in Python, Perl, or R for scripting, statistical programming, and pipeline development.
• Experience developing and deploying applications on UNIX or Linux platforms in a high-performance computing environment.
• Ability to develop and query relational databases such as MySQL or SQLite.
• Experience analyzing next-generation sequencing data types including RNA-seq and ChIP-seq data.
• Experience using version control software such as Git or SVN within a team development workflow.
• Strong written and oral communication skills, including the ability to document technical methods clearly for scientific audiences.

• Advanced degree in Genomics, Bioinformatics, or a related discipline, or a Master's degree with three or more years of specialized research computing experience.
• Knowledge of full-stack web application development using a Python-based framework and a JavaScript front-end library.
• Familiarity with AWS cloud computing services including storage and compute instance management.
• Experience detecting and evaluating copy number variants, structural variants, or chromosomal rearrangements in sequencing data.

• Variant calling pipeline uptime and accuracy rate across active research cohorts.
• Mean time to complete per-sample processing runs on the high-performance computing cluster.
• Proportion of project methodologies covered by reproducible, peer-reviewed documentation.
• Number of research laboratories actively served by maintained genome browsers and analysis pipelines.
• Code review pass rate reflecting adherence to documented standards and validation requirements.
• Typical tools: Variant calling frameworks (commonly GATK or equivalent), scripting environments (commonly Python and Perl), version control (commonly Git)

• Base Salary Range: $80,000 to $115,000 annually depending on degree and experience.
• Bonus: Annual performance bonus of 5 to 10 percent common in research institution settings.
• Equity: Typically not offered in academic or government research contexts.
• Health Benefits: Medical, dental, and vision coverage standard.
• PTO: 15 to 20 days annually plus federal or institutional holidays.
• Common Perks: Conference travel support, publication co-authorship opportunities, and access to institutional HPC resources.

Figures are estimates based on general US market benchmarks and may be outdated. Adjust based on location, company size, and seniority level.

Work authorization in the United States is required for this position, and employment is contingent on successful completion of a background check. All applicants are considered without regard to race, color, religion, sex, national origin, age, disability, veteran status, or any other characteristic protected under applicable federal, state, and local law. Candidates requiring reasonable accommodations during the application or employment process may request them at any time.

The Bioinformatics Programmer owns the development and maintenance of whole-genome and exome variant calling methodologies supporting gene discovery and gene therapy research within NHGRI/DIR, collaborating directly with the NIH Intramural Sequencing Center and high-performance computing teams. This work enables faster identification of disease-causing mutations and ensures reproducible, scalable genomic analysis across multiple intramural and external clinical research partners.

Key Responsibilities

• Develop and maintain whole-genome and exome variant calling methodologies in support of multiple laboratories pursuing gene discovery, gene therapy, and related clinical research projects within NHGRI/DIR.
• Develop and implement variant calling pipelines optimized for high-performance supercomputing environments.
• Design and maintain web-based genome browsers for visualizing aggregate genome and exome data.
• Collaborate with the NIH Intramural Sequencing Center to analyze data from emerging sequencing methodologies.
• Assess researcher needs for large-scale datasets and develop concrete project plans for completion.
• Provide programming and analytic support for bioinformatic pipelines including ChIP-seq and RNA-seq data.
• Write portions of scientific manuscripts and present data in seminars and poster sessions.
• Train bioinformatics trainees in pipeline development and optimization for supercomputing environments.
• Maintain detailed project documentation to ensure reproducibility of all methodologies.

Required Qualifications

• Ph.D. in genomics, bioinformatics, or a related discipline, or a Master's degree with three years of specialized experience as equivalent.
• Minimum two years of post-degree bioinformatics experience including GATK pipeline execution and genotype warehouse development.
• Two years of professional programming experience in Perl, Python, or an equivalent scripting language.
• Experience developing and deploying applications on UNIX or Linux platforms in a high-performance computing environment.
• Knowledge of full-stack web application development using MongoDB, Python Flask, and JavaScript with React and jQuery.
• Experience analyzing next-generation sequencing data types including RNA-seq and ChIP-seq.
• Strong oral and written communication skills with demonstrated success writing scientific manuscripts and presenting at seminars.

Embedded within a bioinformatics team, the Bioinformatics Programmer delivers tools for the management, analysis, and interpretation of omics datasets, executing data processing workflows both locally and in the cloud. Working closely with cross-functional researchers, this role ensures data quality, reproducible pipelines, and clear documentation that support accurate computational analysis outcomes.

Core Functions

• Develop tools for management, analysis, and interpretation of omics data sets.
• Implement and execute omics data processing workflows locally or in the cloud.
• Create standardized summary tables, figures, and listings for omics data.
• Manage large omics dataset collections including cloud import and export and data quality control.
• Write well-documented computer code and conduct code reviews and programming validation.
• Perform workflow benchmarking and identify inconsistencies to initiate resolution of data problems.
• Prepare SOPs, document source code and workflows, and write reports summarizing computational requirements and analysis results.

Qualifications and Experience

• Bachelor's degree in Bioinformatics, Computer Science, or a related field with two years of relevant experience.
• Demonstrated programming skills in Perl, Python, and R for statistical programming.
• Proficiency in Linux and Unix operating system command-line interface.
• Experience developing and querying relational databases such as MySQL or SQLite.
• Familiarity with next-generation sequencing data and open-source bioinformatics tools.
• Experience using Eclipse or other IDEs and version control software such as Git or SVN.
• Familiarity with AWS cloud computing including EC2 and S3 is a plus.
• Strong ability to communicate technical concepts in both written and oral formats.

Reporting to the Bioinformatics R and D team, the Bioinformatics Programmer refines and translates analysis methods into production pipelines within a software platform supporting therapeutic discovery and development. Partnering with multidisciplinary collaborators across lab and cloud environments, this role extends platform capabilities and ensures robust informatics provision from research through production.

Primary Duties

• Write and run production pipelines in a cloud compute environment.
• Integrate company technology and systems from lab to cloud.
• Evaluate and implement new tools and technologies to improve and extend platform capabilities.
• Collaborate in multi-disciplinary projects to ensure informatics provision for therapeutic discovery and development.
• Work with the Bioinformatics R and D team to translate new analysis methods into production.

Skills and Qualifications

• Degree in Bioinformatics or Computer Science.
• Proficiency in Python with a strong software development background.
• Experience with software development best practices including version control and testing.
• Familiarity with Linux and the command line in a bioinformatics context.
• Experience running pipelines on high-performance compute environments including farms, clusters, or cloud.
• Experience with AWS cloud computing and system administration.
• Good communication and presentation skills with flexibility to work in a dynamic environment.