Bioinformatician II - Division of Viral Diseases

Description

IHRC Inc. seeks a dedicated and experienced Bioinformatician II to support our clients at Centers for Disease Control and Prevention (CDC). The Contractor shall provide Bioinformatics II-level technical support for viral genomic surveillance, sequence analysis, laboratory bioinformatics operations, and genomic epidemiology activities with the Division of Viral Diseases (DVD), Viral Vaccine and Preventable Diseases Branch (VVPDB). This position is a remote work location with an ability to travel to CDC location in Atlanta when/if needed. No travel expense is provided. 

• Perform routine and moderately complex bioinformatics analyses, develop and maintain computational workflows, troubleshoot data and pipeline issues, and support scientific and public health surveillance activities under the general direction of senior scientific or bioinformatics staff.
• Develop, revise, document, implement, and maintain standard operating procedures (SOPs), technical procedures, quality documentation, job aids, and other supporting documentation for bioinformatics sequence analysis pipelines and laboratory data-processing workflows.
• Perform production-level quality control, processing, and analysis of next-generation sequencing (NGS) data generated internally and received from external laboratories.
• Process and evaluate common genomic data formats, including FASTQ, BAM/CRAM, VCF, FASTA, and associated sequencing and sample metadata.
• Use commonly accepted bioinformatics software and utilities for sequence alignment, read processing, quality assessment, variant analysis, genome assembly, and visualization. Relevant tools may include, but are not limited to, minimap2, BWA-MEM/BWA-MEM2, Bowtie2, SAMtools, FastQC, MultiQC, iVar, and Integrative Genomics Viewer (IGV).
• Identify, investigate, document, and assist in resolving data-quality issues associated with sequencing outputs, sample and laboratory metadata, pipeline performance, genomic analyses, and data exchange between systems.
• Support routine genomic data-processing workflows from receipt of sequencing data and associated metadata through quality assessment, sequence analysis, review, reporting, archival, and submission to applicable databases or surveillance systems. 
• Develop, configure, test, validate, implement, and maintain reproducible bioinformatics pipelines and workflows for viral sequence analysis using established tools, approved methodologies, version-controlled code, and documented computational environments. 
• Apply Linux-based computational methods and scripting/programming languages to automate, optimize, and troubleshoot bioinformatics workflows. Required technical capabilities shall include experience with Linux command-line environments, Python, R, Bash, Git-based version control, and workflow-management systems such as Nextflow.
• Utilize containerization technologies, such as Docker and/or Apptainer/Singularity, and execute bioinformatics workflows within high-performance computing (HPC) or cluster-based computational environments.
• Provide technical assistance for integrating bioinformatics workflows, genomic data products, laboratory data streams, and metadata with existing laboratory, computational, surveillance, and data-management platforms. 
• Access, use, and support data-management activities within Laboratory Information Management Systems (LIMS) and other systems used to track specimens, sequencing data, analytical results, and associated metadata.
• Apply bioinformatics methods to sequence data generated using both amplicon-based and hybrid-capture NGS approaches for viral pathogens, 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. Relevant tools may include IQ-TREE, RAxML/RAxML-NG, BEAST, Nextstrain, and related phylogenetic or phylodynamic software.
• Analyze genomic surveillance data using phylogenetic, spatiotemporal, epidemiologic, and, as applicable, phylodynamic approaches to characterize viral evolution, transmission patterns, genetic diversity, lineage or clade distributions, and emerging genomic trends.
• Apply mathematical, statistical, and computational approaches, as appropriate to the assigned work, to investigate evolutionary and epidemiological patterns of viruses.
• Support genomic epidemiologic studies evaluating viral evolution and emerging variants, including analyses used to characterize mutations, lineage or clade dynamics, geographic and temporal trends, and other genomic characteristics relevant to public health surveillance and response.
• Evaluate analytical results for consistency with established quality criteria and ensure that genomic analysis methods, procedures, computational workflows, and applicable quality-control measures are performed in accordance with approved protocols and documented procedures.
• Troubleshoot computational issues, data-format inconsistencies, sequence-quality problems, and workflow-processing errors, and document corrective actions or recommended solutions.
• Develop, query, maintain, and validate genomic or sequence-related databases and structured datasets. Experience with SQL and relational database technologies is required or preferred, as applicable to the assigned work. Experience with distributed data-processing or storage technologies, including Hadoop or comparable platforms, may be required for specific assignments.
• Support the 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 one or more assigned viral pathogens or virus families, including technical input regarding sequence-analysis methods, quality considerations, lineage or clade interpretation, surveillance findings, and genomic data products.
• Prepare reports, summaries, dashboards, tables, figures, presentations, and other technical or scientific products that communicate genomic analysis findings, quality metrics, surveillance results, workflow performance, or project accomplishments.
• Contribute technical content, analyses, figures, methods, and supporting 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 genomic surveillance requirements and support completion of assigned scientific and technical activities.

Requirements

• Experience performing bioinformatics analysis in a research, clinical, public health, or comparable scientific environment.
• Experience independently executing established analytical workflows and perform moderately complex bioinformatics assignments with general technical direction.
• Next-generation sequencing data processing and quality control.
• Amplicon-based and/or hybrid-capture sequencing methods.
• Viral genome assembly, reference-based analysis, consensus generation, and variant analysis.
• Linux command-line environments.
• Python, R, and Bash scripting.
• Git or comparable version-control systems.
• Reproducible workflow development using Nextflow or comparable workflow-management systems.
• Docker and/or Apptainer/Singularity containerization.
• HPC or cluster computing environments.
• Phylogenetic analysis and associated software.
• Genomic epidemiology or pathogen genomic surveillance.
• Management and analysis of sequencing metadata.
• LIMS or comparable laboratory/data-management systems.
• SQL and relational database concepts.
• Experience with Hadoop or comparable distributed data-processing technologies and experience developing or optimizing      genomic databases are desirable when applicable to the assigned work.

Education

• MS with 1-3 years of experience or a PhD/post-doc with at least 1 year of experience.