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.
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
- 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
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
- 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.