Bioinformatics SME II

 Eagle Global Scientific (EGS) is seeking a Bioinformatics SME to provide the following:

• Construct pipelines and workflows for sequence analysis and build custom algorithms and tools for specific problems •
• Conduct genomic epidemiologic studies on the evolution of viruses to detect and assess the risk of new emerging variants to current vaccines 
• Analyze next generation sequence data from routine and enhanced global surveillance using spatiotemporal, phylodynamic, and epidemiologic approaches to determine trends that can be used in making decisions about prevention, treatment and control of epidemics or pandemics 
• Use mathematical and computational approaches to understand the evolutionary and epidemiological patterns of viruses 
•  Ensure the appropriate genomic analysis methods, procedures, techniques, and applicable quality controls are correctly conducted by referring to standard protocols 
•  Prepare reports, summaries, presentations, papers and other documents to highlight findings, accomplishments, and surveillance data
• Genome assembly of next generation sequencing from Illumina required, PacBio and Minion (all three preferred)
• Experience with Integrative Genomics Viewer (IGV) and samstools
• Experience with Linux, command-line interfaces, and automation via Shell scripting 
• Experience in programming (R, Python, Perl, etc.), version control (GIT) & best practices
• Understanding of data management fundamentals (SQL, relational model, OLAP)
• Knowledge of workflow management tools (Snakemake, Nextflow) a big plus
• Familiarity with business intelligence tools (Tableau, PowerBI)
• Exposure and literacy with distributed and parallel computing (Spark, Hadoop, AWS (Amazon web service), Grid Engine / HPC (High Performance Computing)) is greatly preferred