Please note that this position is contingent upon the successful award of a contract currently under bid.

Summary:

GbILS is seeking a Bioinformatician to support sequencing analytics, bioinformatics pipeline development, and computational data management.  This position will develop, implement, and maintain bioinformatics workflows that process and analyze high-throughput sequencing data while collaborating with multidisciplinary teams to generate actionable public health insights. The Bioinformatician will work under the guidance of senior scientific staff while independently managing assigned analytical projects.

Essential Job Functions:

The Bioinformatician implements and maintains established bioinformatics workflows, performs routine and specialized genomic analyses, and supports outbreak response and surveillance activities under the guidance of senior staff. This role executes core analytical tasks while contributing to pipeline development and database management. 

• Bioinformatics Analysis:
  • Develop, implement, maintain, and optimize bioinformatics workflows
  • Perform quality control, assembly, annotation, and analysis of environmental metagenomic sequencing data
  • Analyze whole genome sequencing and metagenomic datasets using established computational methods
  • Develop statistical methods to identify variants and estimate pathogen abundance from sequencing datasets
  • Generate standardized bioinformatics outputs for integration into surveillance platforms
  • Support the validation and testing of bioinformatics workflows and analytical pipelines
• Data Management & Infrastructure:
  • Manage high-throughput sequencing raw and processed data, databases, and uploads to sequencing repositories
  • Support maintenance and optimization of cloud-based and high-performance computing environments used for bioinformatics analyses
  • Implement quality assurance and quality control procedures throughout bioinformatics workflows.
  • Assist with improving computational performance for high-volume sequencing datasets
• Wastewater & Environmental Metagenomics: 
  • Implement and execute bioinformatics pipelines for quality control, assembly, and analysis of wastewater and environmental metagenomic sequencing datasets, including preprocessing, taxonomic classification, and abundance estimation
  • Perform assembly and annotation of metagenomic sequences; apply tools such as SPAdes,  Bowtie2, minimap2, prokka/bakta, and related tools for read processing, contig assembly, and gene prediction 
  • Maintains and updates curated environmental metagenomics reference databases organized by source type and organism group (microbial, viral, fungal, eukaryotic) to support detection and characterization workflows
  • Assist with waterborne and environmental outbreak response by processing and analyzing sequencing data from outbreak samples in a timely manner
• Pathogen Characterization & Source Attribution: 
  • Execute metagenomic source attribution analyses using established pipelines, interpreting results to support public health investigations and preparing summary outputs for review by senior bioinformaticians and program staff 
  • Perform in silicodetection and characterization assays for environmental NGS datasets to assist with diagnostics research and development 
•  Whole Genome Sequencing – Viral Pathogens: 
  • Perform quality control, reference-based assembly, variant calling, and annotation of viral WGS data (e.g., measles virus) using established workflows; flag anomalies and quality issues for senior review 
  • Support phylogenetic analyses of viral genomes, generating trees and summary statistics using open-source tools under the direction of senior bioinformatics staff
• Pipeline Execution & Maintenance: 
  • Run and monitor Nextflow pipelines within HPC and cloud computing environments; troubleshoot execution errors and document issues and resolutions 
  • Develops and refines pipeline components, contributing modular scripts and workflow steps that align with established standards
  • Manage high-throughput sequencing raw data and analytic files, including uploads to NCBI and other sequencing repositories, ensuring metadata completeness and accuracy
•  Scripting & Analysis Support:
  • Write and maintain Python, R, and Bash scripts for data processing, format conversion, and analytical tasks within Linux environments 
  • Performs database queries and routine data management tasks across relational (PostgreSQL, MySQL) and NoSQL (MongoDB) database systems
  • Maintain code using Git/GitHub/GitLab; follow documentation standards established by senior staff 
• Reporting & SoPs: 
  • Prepare clear, accurate reports and presentations summarizing sequencing analysis results and quality metrics for internal program use 
  • Develops and updates standard operating procedures (SOPs) for bioinformatics analyses across wastewater, environmental, and isolate-based workflows 
  • Support manuscript preparation and data submission for peer-reviewed journals and scientific conferences as directed 
•  Software Evaluation: 
  • Identify, assess, and qualify software solutions designed to support the execution of bioinformatics workflows and analyses  
  • Conduct structured comparative evaluations of candidate tools, encompassing output quality, feature sets, computational resource utilization, and operational stability, leveraging industry-standard benchmarks and, where appropriate, task-specific performance metrics. Synthesize evaluation findings into clear, actionable summaries and deliver expert recommendations to team members and organizational leadership regarding optimal and alternative strategies  
  • Maintain continuous engagement with the scientific literature to proactively identify emerging methodologies and software tools relevant to bioinformatics operations and communicate pertinent developments and strategic alternatives to team members and leadership in a timely manner 

Necessary Skills and Knowledge:

• Strong Python programming skills with experience in bioinformatics data analysis
• Familiarity with database design principles and data management
• Knowledge of distributed computing and parallel processing concepts is preferred
• Ability to troubleshoot analytical workflows and resolve computational issues
• Ability to work independently while collaborating effectively within multidisciplinary teams

Minimum Qualifications:

• Minimum 2-5 years of related experience
• Experience implementing and maintaining bioinformatics pipelines
• Experience working with sequencing data and genomic analyses
• Experience creating visualizations using Python or R (ggplot2)
• Experience using Git-based version control systems

Preferred Qualifications:

• Proficiency in Python, R, and Bash in Linux/HPC environments 
• Working experience with Nextflow; familiarity with Snakemake or similar workflow managers 
• Containerization: Docker, Singularity 
• NGS tools: Bowtie2, SPAdes, minimap2, prokka/bakta, and related open-source bioinformatics tools 
• Code versioning: Git, GitHub, GitLab 
• Familiarity with NCBI data submission standards and cloud computing environments 
• Experience supporting federal government programs, preferably CDC, is preferred

Pay and BenefitsAt Goldbelt, we value and reward our team's dedication and hard work. We provide a competitive base salary commensurate with your qualifications and experience. As an employee, you'll enjoy a comprehensive benefits package, including medical, dental, and vision insurance, a 401(k) plan with company matching, tax-deferred savings options, supplementary benefits, paid time off, and professional development opportunities.