Job Description Summary Performs software programming for applied clinical genomics team. Maintains and runs software systems for bioinformatics analysis which can include raw data quality control, sequence alignment, variant calling, annotation and reporting. Provides input to develop software and data analysis solutions. Assists with project documentation, defining and implementing operational and business objectives, especially with respect to cutting-edge data analysis methods. Completes department tasks and provides ongoing support for existing databases/software.
Responsibilities: Performs software programming for applied clinical genomics team. In collaboration with bioinformatics specialists, maintains and runs, software systems for bioinformatics processing of sequence data, including, but not limited to, raw data quality control, sequence alignment, variant calling, annotation and reporting. Develops and implements workflows for specific genomic data analysis tools in collaboration with research scientists. Develops practices to manage efficient operation of workflows. Builds and deploys data analysis support systems for large data sets; e.g., well-structured flat files, APIs, or other types of services. Develops robust, efficient and fault tolerant bioinformatics analysis pipelines using scripting languages within a Linux environment. Acquires, cleans, and structures data from multiple sources to ensure data quality. Develops web-base and SQL database application to aid variant visualization, variant annotation, and pathologic report generation Possible weekend and evening remote work necessary to perform clinical data analysis and system monitoring
Education: Bachelor's Degree in Systems Biology, Bioinformatics, Computer Science or related field (such as Mathematics, Physics, Biology, Business Intelligence).
Certifications: None required.
Complexity of Work: Requires critical thinking skills, decisive judgment, and the ability to work with minimal supervision. Must be able to work in a stressful environment and take appropriate action. Ability to participate within a multidisciplinary team of IT professionals, physicians, molecular biologists, computer scientists, and biostatisticians.
Work Experience: Experience in genomics or bioinformatics software, or analyzing next generation sequencing. Detailed knowledge of core bioinformatics concepts and skills (including sequence alignment, genome browsers, next-generation sequencing data formats, association studies, public resources, network/pathway driven analysis, and quality control principles). Proficiency in interpreted languages; Python or Perl preferred. Experience or willingness to learn R for specialized tasks and integration with data analytics workflows. Strong background in Linux/UNIX operating system environment, including BASH scripting. Experience producing useful code (not necessarily in context of employment - personal projects or contributions to open-source projects are applicable). Experience with high performance computing cluster preferred.
Preferred Qualifications: Master's Degree in Biomedical Informatics
Physical Requirements: Requires extensive sitting and dexterity to perform work on a PC/laptop/other workstation; normal or corrected vision to use computer monitor; ability to clearly communicate verbally by phone and in person.
Personal Protective Equipment: Follows Standard Precautions using personal protective equipment.
Keywords: Bioinformatics, Python, Perl, Linux, Unix, BASH