Bioinformatics DevOps Engineer/Developer - Advanced Molecular Detection
WiredPeople
- Jacksonville, FL
- Permanent
- Full-time
- Plan and execute whole-genome sequencing analysis, comparative genomic analysis, and other analytic research projects, establishing new standard operating procedures (SOPs) by developing custom bioinformatics pipelines/workflows.
- Select and develop appropriate analysis techniques and measures and identify and implement the necessary software and databases to complete defined analytical tasks.
- Develop, manage, and curate databases for analysis.
- Identify, implement, and maintain data quality control, data submissions and management programs.
- Lead the development and implementation of a cloud computing architecture to improve and expand our current computational infrastructure.
- Provide telephonic and web based technical assistance to other bioinformaticians, laboratory staff, and epidemiologists on the use of complex data analysis techniques and methods.
- Provide approved updates with analytical results from developed bioinformatic pipelines to be disseminated to laboratory and epidemiological staff.
- Lead and coordinate with other bioinformaticians involved in analysis projects, including data sharing and engagement across multidisciplinary project teams.
- Disseminate approved results of research projects in a wide range of venues including publications, peer reviewed journals, summaries, manuscripts, special reports, and oral/poster presentations.
- Attend approved training workshops and complete a corresponding report on the training received.
- A PhD in bioinformatics, genomic epidemiology, microbiology, virology, parasitology, evolutionary biology, microbial genetics, molecular biology, computer science, or related field.
- At least five years of practical and technical experience in microbial and/or public health bioinformatics.
- At least five years of experience with bioinformatic development of pipelines for the phylogenetic and comparative genomic analysis of microbial organisms.
- At least two years of experience with cloud computing.
- Bioinformatics experience with microbiology and/or public health applications.
- Experience working in a UNIX/LINUX environment and writing shell scripts.
- Proficiency in at least one scripting/programming language (e.g., Python, Perl, R, C++, Java) and willingness to learn new languages, if necessary.
- Experience developing custom scripts and executing command-line bioinformatics tools for microbial genomics comparative analysis (i.e., assembly, annotation, variant detection, multiple sequence alignment, phylogenetic tree building, pairwise SNP matrices, etc.).
- Experience in phylogenetics and interpreting comparative genomic data from microbial organisms.
- Experience using git/github.
- Experience querying and submitting genomic data from/to NCBI databases.
- Excellent verbal communication with experience presenting complex, technical data to multidisciplinary teams.
- Excellent written communication and experience publishing in the relevant scientific literature.
- Strong background in phylogenetics of bacterial and/or viral pathogens.
- Proficiency in Python and R.
- Experience analyzing NGS data generated from Illumina, Oxford Nanopore, and PacBio platforms.
- Experience with high-performance computing (HPC) and/or cloud computing.
- Experience with Singularity and/or Docker.
- Experience with Conda.
- Experience developing and/or executing workflows using a workflow language (such as Snakemake, Nextflow, WDL).
- Experience with pathogen genomics, especially of public health concern.