Bioinformatician

Goldbelt, Inc.•Atlanta, GA

About The Position

Goldbelt Integrated Logistics Services (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. This position is contingent upon the successful award of a contract currently under bid.

Requirements

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
Strong Python programming skills with experience in bioinformatics data analysis
Familiarity with database design principles and data management
Ability to troubleshoot analytical workflows and resolve computational issues
Ability to work independently while collaborating effectively within multidisciplinary teams

Nice To Haves

Knowledge of distributed computing and parallel processing concepts is preferred
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

Responsibilities

Implement and maintain established bioinformatics workflows.
Perform routine and specialized genomic analyses.
Support outbreak response and surveillance activities.
Execute core analytical tasks while contributing to pipeline development and database management.
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.
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.
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.
Maintain and update 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.
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 silico detection and characterization assays for environmental NGS datasets to assist with diagnostics research and development.
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.
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.
Write and maintain Python, R, and Bash scripts for data processing, format conversion, and analytical tasks within Linux environments.
Perform 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.
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.
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.