WiredPeople is hiring a
Bioinformatics DevOps Engineer/Developer

Summary

The job is for a Bioinformatics DevOps Engineer/Developer at WiredPeople who will support genomic surveillance and outbreak investigations. The role involves planning and executing whole-genome sequencing analysis, developing custom bioinformatics pipelines, managing databases, providing technical assistance, leading development of cloud computing architecture, and disseminating research results.

Requirements

• 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

Responsibilities

• Plan and execute whole-genome sequencing analysis
• Develop custom bioinformatics pipelines/workflows
• Select and develop appropriate analysis techniques and measures
• Identify and implement the necessary software and databases to complete defined analytical tasks
• Develop, manage, and curate databases for analysis
• Lead the development and implementation of a cloud computing architecture
• Provide telephonic and web based technical assistance to other bioinformaticians, laboratory staff, and epidemiologists
• 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

Preferred Qualifications

• 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