Job:CDC Bioinformatics position

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[Alison Halpin]

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Come join our team at CDC working to prevent and respond to healthcare-associated infections and antimicrobial resistance.

ESSENTIAL JOB FUNCTIONS:

• Maintain, de-bug, execute and improve bioinformatics tools and pipelines used in-house, including implementation of workflow manager programs (e.g., nextflow)
• Build new bioinformatics tools and pipelines as appropriate, including creating containers for applications (e.g., docker, singularity)
• Maintain updated git account documenting scripts and programs.
• Analyze sequence data from scientific projects and programs of bacterial isolates using appropriate programs and bioinformatics tools and pipelines, including: Quality assessment of next generation sequence data; Analyses for identification and subtyping of healthcare-associated and emerging bacterial pathogens;
• Identify, validate, and implement methods and procedures to analyze next generation sequencing data, including methods for characterization and phylogenetic analyses and adjustments in methods and procedures as appropriate.
• Coordinate sequence data sharing with requestors and collaborating laboratories.
• Manage incoming sequence data for processing, documentation, tracking, and inventory as needed.
• Integrate laboratory (conventional and next generation), clinical, and epidemiologic data generated to provide analyses of data from healthcare-associated infection and other emerging pathogen studies and investigation.
• Develop new and improved concepts, principles, and techniques that will advance the body of knowledge of information management.
• Apply advanced computer science methods and techniques to solve complex computer processing requirements for data analysis, inventory management and clinical system interface.
• Enhance existing data systems; edit, proofread, and critique team members in a professional manner.

NECESSARY SKILLS & EXPERIENCE:

• Highly proficient or possess extensive experience with Bash (no exceptions)
• Highly proficient or possess extensive with Python (no exceptions)
• Must be proficient with common bioinformatics open-source tools (e.g., samtools, bcftools, bwa-mem), HPC (high performance computing), and NCBI.
• Proficient with tools to elucidate mobile genetic elements from short read data (e.g., PlasFlow).
• Self-motivated with a strong attention to detail and accuracy.
• Fluent English in written, verbal, and interpersonal exchanges.

MINIMUM QUALIFICATIONS:

• Bachelor’s degree in Biostatistics, Statistics, Epidemiology, Public Health, or related field.
• 3 - 8 years’ relevant experience in a Bioinformatics role.

PREFERRED QUALIFICATIONS:

Master’s degree in Biostatistics, Statistics, Epidemiology, Public Health, or related field.

• Experience with Oxford Nanopore technology (e.g., MinION) platform bioinformatics analyses.
• Experience with nextflow or other workflow manager programs, creating containers for applications (e.g., docker, singularity), Git (i.e., GitLab, GitHub), frameworks for storing and processing large data sets (e.g., Hadoop).
• Experience with tools to elucidate mobile genetic elements from short read data (e.g., PlasFlow).
• Cloud migration and integration is a huge plus.