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