Bioinformatics Programmer

Primary Purpose:

We are seeking a talented and motivated Bioinformatics Programmer to join our team and play a key role in developing automated scalable data processing and analysis pipelines in the AWS cloud. You will be responsible for developing and automating omics and other clinical data processing, analysis, and reporting pipelines. You will work closely with cross-functional teams, including data scientists, bioinformatics analysts, bioinformatics data managers, software engineers, and product managers, to bring complex analytical solutions to life and drive clinical Design, develop, and implement software solutions for analyzing and interpreting omics data (genomics, transcriptomics, proteomics, etc.) in AWS.

- Develop automated workflows for data processing and analysis for -omics and other clinical data using workflow management software such as SnakeMake in combination with shell scripting and R, and Python programming.

- Integration of workflows with AWS Services such as AWS CLI, S3, Batch, and Cloud Watch.

- Apply statistical and machine learning techniques to extract meaningful insights from large-scale omics datasets.

- Automate table, listing, and figure generation and reporting using a combination of R Markdown, R Knitr, and LaTeX.

- Build interactive analysis reports using R Shiny.

- Execute, troubleshoot, and benchmark data processing, analysis, and reporting workflows.

- Write well-documented computer code, conduct code reviews, and programming validation.

- Identify inconsistencies and initiate resolution of data, analytical, or reporting problems.

- Other responsibilities as assigned.

Qualifications:

- Bachelor's degree in Bioinformatics, Computer Science, or a related field, and 3 to 8 years relevant Competent in using Linux command line interface and scripting.

- Demonstrated computer programming skills in Python as well as R for statistical programming

- Experience using RStudio (or other IDEs) and Version Control software (Git, SVN, or similar) to manage programming code.

- Understanding of basic biological principles and omics technologies.

- Familiarity with next-generation sequencing data and open-source bioinformatics tools

- Ability to manage multiple tasks

- Ability to work independently, as well as in a team environment

- Ability to effectively communicate technical concepts, in both written and oral format

- Experience using SnakeMake for workflow development.

- Ability to query relational databases using SQL.

- Familiarity with AWS cloud computing (AWS EC2, S3, Batch, CloudWatch).

- Building interactive web applications using R Shiny is a plus.