SCOPE OF WORK

We are seeking a highly motivated and detail-oriented bioinformatician to support genomic surveillance, outbreak response, and research activities for bacterial pathogens, including Streptococcus, Legionella, Mycoplasma, Escherichia coli, and Chlamydia. The ideal candidate will have experience with analyzing whole-genome and metagenomic sequencing data, maintaining and developing bioinformatics pipelines, supporting data interpretation, and serving as a resource for non-bioinformatician collaborators.

REQUIRED QUALIFICATIONS:

• Master’s degree or higher in bioinformatics, microbiology, biological sciences, or a related field.
• Proficiency in Python, R, Bash, and common bioinformatics tools (e.g., BWA, samtools, snippy, spades, Flye, Medaka).
• Experience working with whole-genome and metagenomic sequencing data generation and analysis, particularly in microbial genomics.
• Familiarity with public sequence databases (NCBI, pubMLST) and sequence data submission protocols.
• Experience with ONT platforms and software is a plus.
• Strong communication and collaboration skills, especially with multidisciplinary teams.
• Ability to document workflows, write clear scripts/job aids, and support knowledge transfer.

PREFERRED QUALIFICATIONS:

• Experience with building and maintaining reproducible workflows using workflow managers (e.g., Nextflow, Snakemake).
• Background in microbial genomics, vaccine target evaluation, or public health microbiology.
• Previous experience in mentoring or supporting non-bioinformaticians.

LANGUAGE SKILLS:

• The candidate must possess excellent oral and written communication skills in English.
  REQUIREMENT: Must be a United States citizen or permanent resident or have authorization for employment in the United States.
  SALARY: Commensurate with qualifications and experience.

TRAVEL: AS REQUIRED TO FULFILL THE RESPONSIBILITIES OF THE POSITION

ASRT, Inc. provides scientific, information management, management consulting, bioinformatics, and administrative program support to the Centers for Disease Control and Prevention (CDC) and other Federal and private sector clients. The successful candidate will be a full-time employee of ASRT, Inc., and will be assigned to the Pneumonia and Streptococcus Laboratory Branch (PSLB), Division of Bacterial Diseases (DBD), National Center for Immunization and Respiratory Diseases (NCIRD), at the CDC, located at 1600 Clifton Road, Atlanta, GA.

MAJOR DUTIES AND RESPONSIBILITIES

• Execute and manage bioinformatics pipelines to analyze next-generation sequencing (NGS) data; curate and prepare pipeline outputs for review by technical leads.
• Communicate with computing system administrator and technical leads to help address pipeline non-compliance events.
• Submit sequencing data to public repositories; verify and submit new sequences to relevant databases.
• Conduct genomic analyses to characterize pathogens of interest for surveillance and research.
• Develop and maintain databases that integrate sequencing results with associated meta data to support tracking and retrieval.
• Maintain and validate existing pipelines across multiple pathogens; ensure documentation and reproducibility.
• Develop custom scripts and job aids to support analysis of sequencing data from various platforms, including long-read sequencing data, culture-independent sequencing data, and metagenomics sequencing data.
• Assist in data visualization, interpretation and reporting of NGS results; contribute to scientific communication and manuscript development.
• Serve as a point-of-contact for peer-to-peer bioinformatics support, helping microbiologists with ad hoc data analysis needs and sequence-related queries.
• Provide consultation and informal training to non-bioinformatician colleagues to enhance cross-disciplinary collaboration and bioinformatics literacy.
• Contribute to developing a community of practice within the branch for NGS work.
  Requirements: