Bioinformatics Pipeline Automation Engineer – Texas A&M Genomics & Bioinformatics Service

Job ID:
Job date: 2018-04-03
End Date:

Company : TGT

Country :

Role : Technician

Job Description:
This job will have the following responsibilities:

Run the existing variant analysis pipeline on production samples, while working to improve the automation of the pipeline
Work with scientists adapting the pipeline to a range of new uses to identify and test needed modifications
Work with scientists and engineers working to develop a new, more flexible variant pipeline and the tools needed to evaluate and compare the results of different variant calling approaches.

Qualifications & Requirements:

Master’s degree in Bioinformatics, Genomics, Genetics, Computer Sciences or a related field, or a Bachelor’s with equivalent experience.
Demonstrated programming and scripting skills in R and Python.
Experience with Unix/Linux computing environments
Familiarity with NGS sequencing data and tools commonly used in sequence analysis for read trimming, alignment, and variant calling
Ability to handle and manipulate large datasets.
Demonstrated curiosity and ability to innovate.

Must haves:

Curiosity about the scientific problems we are trying to solve
Communication skills for working effectively with a diverse, distributed team and customers.

Technical skills:

Ability to run a complex bioinformatics pipeline in the cloud at scale
Engineering skill, to make that task easier through improved automation.
Analysis skills – statistical and software – to help build tools to compare the results of multiple approaches to variant analysis and improve the pipeline.

Highest level of education: A Ph.D. wouldn’t be completely out of place, but a master’s level scientist or engineer could do the job.

3-5 daily responsibilities:

A day in this role would include both operational tasks and work on pipeline development.

Responsibilities:

Run samples through the variant-calling pipeline as they become available for analysis.
Improving the automation of the pipeline so that time per sample goes down.
Working with the group that is developing a more modern pipeline to test and validate the new pipeline and build tools to assist in comparing the results of different approaches.

Soft skills:

Ability to communicate effectively with a community of scientists, software developers, and data analysts
Eagerness to learn both the science and software tools needed in the role.

Who will this person work with on a daily basis

There are several different kinds of collaborators:

Members of the SNP pipeline team. This includes people in Analytics and Data Science, Molecular Breeding, Breeding and Vegetables who collaborate closely to define and implement the pipeline
Scientists who have submitted samples for analysis. The contractor will ask researchers about their projects when information is needed to make the right analysis choices and communicate with them about analysis results.
We also work closely with IT to deliver pipeline output to enterprise systems.

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Additional Info:
Job Types: Full-time, Contract