Bioinformatician

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

Overview Please note that this position is contingent upon the successful award of a contract currently under bid. GbILS provides four specific areas of expertise—Logistics Engineering, Measurement Sciences, Program Management, and Technical Support—serving the scientific, technical, and engineering needs of clients. GbILS values its innovative thinking and service-oriented team who provide services for a variety of federal government and commercial clients.

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…