OVERVIEW

• Evaluating and choosing among existing laboratory protocols and workflows for conducting whole genome sequencing (WGS) of viral genomes, in terms of throughput, quality, cost, effectiveness, and efficiency.
• Determining which of the existing NGS platforms is most suitable for efficient viral sequencing, and then using the optimized protocol and platform in collaboration with CDC scientists to generate pilot sequencing data for input into a bioinformatics assembly and analysis pipeline.
• Helping Bioinformatics Scientists to design and implement such a pipeline, as well as to comment on standard bioinformatics analyses to generate useful data for public health purposes and the user-friendliness of the developed graphical user interfaces. Depending on the background in bioinformatics, successful applicant would participate in the development of these analysis pipelines as well.
• Ideally, this position requires some prior competency in translating NGS results into meaningful biological insights using contemporary methods including variant analysis, comparative genomics, phylogenetic methods, and integration with other information types.

RESPONSIBILITIES

• Evaluating and selecting existing laboratory protocols for viral whole-genome sequencing, comparing quality, efficiency, cost, and throughput of the protocol.
• Being a key member in determining which existing NGS platforms are best suited for efficient sequencing of RNA viruses
• Building and supporting cutting-edge pipelines for the analysis and interpretation of NGS data including sequence production, metagenomics, evolutionary genomics, variant calling, and interpretation.
• Participating in the technical development process of an emerging NGS analytic and surveillance platform by optimizing protocols and platforms used in the implementation and enhancement of the analytic pipelines.
• Maintaining up-to-date expertise in the science and application of genomic technologies.
• Providing professional grade reports on ongoing sequencing, assembly, and analysis activities.

REQUIREMENTS

• M.S. or Ph.D. in molecular biology, virology, biochemistry, or related fields and 5-7 years' experience or equivalent combination of education and experience.
• 2+ years' direct, hands-on experience in Next Generation Sequencing (NGS) protocol and platform use (with more than one platform).
• Excellent written and spoken communication skills.
• Basic experience with primary NGS data analysis (e.g. Run Quality evaluation).

PREFERENCES

• Laboratory experience in choosing among NGS protocols and platforms (e.g. Illumina, IonTorrent, PacBio, and Oxford Nanopore) for different organisms, including library creation and loading optimization of RNA-derived samples.
• Experience with basic NGS run and sequence analysis methods, workflows, and pipelines.
• Experience with and/or knowledge of Open Source and COTS software used for such assembly and analysis.
• Comfortable working in a dynamic, fast paced environment.
• Skills in software requirements development; any experience programming in Perl, Python, or R would be a real plus.

LOCALE

HOW TO APPLY

DEADLINE