Bioinformatician II - Division of Viral Diseases

IHRC INCORPORATED•Atlanta, DE

3d•Remote

About The Position

IHRC Inc. seeks a dedicated and experienced Bioinformatician II to support clients at the Centers for Disease Control and Prevention (CDC), within the Division of Viral Diseases (DVD), Viral Vaccine and Preventable Diseases Branch (VVPDB). The position provides technical support for viral genomic surveillance, sequence analysis, laboratory bioinformatics operations, and genomic epidemiology. Work is remote, with the ability to travel to a CDC location in Atlanta when needed; travel expenses are not provided. Under the general direction of senior scientific or bioinformatics staff, the role performs routine and moderately complex bioinformatics analyses, develops and maintains computational workflows, troubleshoots data and pipeline issues, and supports scientific and public health surveillance activities. The Bioinformatician processes and analyzes next-generation sequencing data from internal and external laboratories; supports workflows from data receipt through quality assessment, analysis, reporting, archiving, and submission; and develops, validates, implements, and maintains reproducible viral sequence-analysis pipelines. The role applies Linux-based computational methods and Python, R, and Bash scripting; uses Git, workflow-management systems such as Nextflow, containers such as Docker or Apptainer/Singularity, and HPC or cluster environments. It supports laboratory and surveillance data integration, LIMS and metadata activities, viral phylogenetic and genomic epidemiologic analyses, and the maintenance of genomic databases and structured datasets. The position also evaluates analytical quality, documents procedures and corrective actions, prepares technical and scientific materials, and collaborates with laboratory scientists, epidemiologists, bioinformaticians, data scientists, informaticians, and other project personnel.

Requirements

Experience performing bioinformatics analysis in a research, clinical, public health, or comparable scientific environment.
Experience independently executing established analytical workflows and performing moderately complex bioinformatics assignments with general technical direction.
Experience processing and performing quality control on next-generation sequencing data.
Experience with amplicon-based and/or hybrid-capture sequencing methods.
Experience with viral genome assembly, reference-based analysis, consensus generation, and variant analysis.
Experience with Linux command-line environments.
Experience using Python, R, and Bash scripting.
Experience with Git or comparable version-control systems.
Experience developing reproducible workflows using Nextflow or comparable workflow-management systems.
Experience with Docker and/or Apptainer/Singularity containerization.
Experience with HPC or cluster computing environments.
Experience with phylogenetic analysis and associated software.
Experience with genomic epidemiology or pathogen genomic surveillance.
Experience managing and analyzing sequencing metadata.
Experience with LIMS or comparable laboratory/data-management systems.
Experience with SQL and relational database concepts.
Education and experience: MS with 1–3 years of experience, or PhD/post-doc with at least 1 year of experience.

Nice To Haves

Experience with Hadoop or comparable distributed data-processing technologies.
Experience developing or optimizing genomic databases.

Responsibilities

Perform routine and moderately complex bioinformatics analyses and support viral genomic surveillance, sequence analysis, laboratory bioinformatics operations, and genomic epidemiology.
Develop, revise, document, implement, and maintain SOPs, technical procedures, quality documentation, job aids, and supporting documentation for bioinformatics pipelines and laboratory data-processing workflows.
Perform production-level quality control, processing, and analysis of NGS data generated internally and received from external laboratories.
Process and evaluate genomic data formats, including FASTQ, BAM/CRAM, VCF, and FASTA, along with sequencing and sample metadata.
Use bioinformatics software and utilities for sequence alignment, read processing, quality assessment, variant analysis, genome assembly, and visualization.
Identify, investigate, document, and help resolve data-quality issues involving sequencing outputs, sample and laboratory metadata, pipeline performance, genomic analyses, and data exchange.
Support genomic data-processing workflows from receipt of sequencing data and metadata through quality assessment, sequence analysis, review, reporting, archiving, and submission to databases or surveillance systems.
Develop, configure, test, validate, implement, and maintain reproducible bioinformatics pipelines and workflows for viral sequence analysis using established tools, approved methods, version-controlled code, and documented computational environments.
Apply Linux-based methods and scripting or programming to automate, optimize, and troubleshoot bioinformatics workflows.
Use containerization technologies and execute workflows in HPC or cluster-based computational environments.
Support integration of bioinformatics workflows, genomic data products, laboratory data streams, and metadata with laboratory, computational, surveillance, and data-management platforms.
Access and support data-management activities in LIMS and other systems that track specimens, sequencing data, analytical results, and metadata.
Analyze viral pathogen data from amplicon-based and hybrid-capture NGS approaches, including read processing, reference-based analysis, assembly, consensus generation, variant identification, and quality assessment.
Conduct phylogenetic and genomic epidemiologic analyses of viral pathogens using appropriate computational approaches and software.
Analyze genomic surveillance data using phylogenetic, spatiotemporal, epidemiologic, and, where applicable, phylodynamic approaches to characterize viral evolution, transmission patterns, genetic diversity, lineage or clade distributions, and emerging trends.
Apply mathematical, statistical, and computational approaches to investigate viral evolutionary and epidemiological patterns.
Support genomic epidemiologic studies of viral evolution and emerging variants, including analyses of mutations, lineage or clade dynamics, geographic and temporal trends, and other public-health-relevant genomic characteristics.
Evaluate analytical results against established quality criteria and ensure methods, procedures, workflows, and quality controls follow approved protocols and documented procedures.
Troubleshoot computational issues, data-format inconsistencies, sequence-quality problems, and workflow errors; document corrective actions or recommended solutions.
Develop, query, maintain, and validate genomic or sequence-related databases and structured datasets.
Support development and optimization of relational databases used to manage genomic sequence data, analytical outputs, laboratory metadata, or surveillance information.
Provide genomic subject-matter support for assigned viral pathogens or virus families, including input on methods, quality considerations, lineage or clade interpretation, surveillance findings, and genomic data products.
Prepare reports, summaries, dashboards, tables, figures, presentations, and other products communicating analysis findings, quality metrics, surveillance results, workflow performance, or project accomplishments.
Contribute technical content, analyses, figures, methods, and documentation to abstracts, posters, presentations, technical reports, manuscripts, peer-reviewed publications, and other scientific or surveillance products.
Collaborate with laboratory scientists, epidemiologists, bioinformaticians, data scientists, informaticians, and other project personnel to address surveillance requirements and complete assigned work.