Job:CDC Bioinformatics position
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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.
CDC python git bioinformatics bash • 323 views
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