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Pipeline/Integration Engineer - Lewisville, TX in Lewisville, TX at Quest Diagnostics

Date Posted: 2/5/2019

Job Snapshot

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Job Description

Look for more than answers.


At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast moving career opportunities where you can affect change at a rate unheard of in many organizations of our size and scope. While we invest in and develop technology to drive our innovations, our ongoing success relies on our people.

As a Pipeline/Integration Engineer you will work for the world leader in the industry, with a career where you will have the opportunity to collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a market that is growing and developing.

Pipeline/Integration Engineer – the role

MedFusion is a Quest Diagnostics Precision Oncology Center of Excellence and a full-service laboratory and clinical trials service organization. Our core oncology products provide specific answers that clinicians need to deliver the appropriate diagnostic and/or prognostic care to oncology patients throughout the United States.

As a member of the MedFusion/Quest Diagnostics Bioinformatics team, you will focus on the full life cycle of clinical-grade next-generation sequencing (NGS) pipelines applied to both solid tumors and hematological malignancies – from design and development to implementation and integration – ensuring maximal accuracy for patient care.

Job responsibilities:

  • Work in collaboration with key scientific personnel to build, test, adapt, support and validate clinical-grade variant analysis pipelines with integration into our production system (LIMS)

  • Participate in pipeline standardization across multiple partner sites

  • Maintain current NGS production pipeline(s)

  • Report directly to the Bioinformatics Scientific Director

To qualify, the ideal candidate will have the following skills and experience: •        

  • B.S. with 6+ years of experience in Bioinformatics, Genomics, Genetics, Computer Sciences or a related field; M.S. with 4+, or Ph.D. with 2+ years of experience, or equivalent Desired Qualifications  

  • Proficiency building, running and monitoring genomic analysis pipelines

  • Proficiency in manipulating large NGS sequencing datasets: data transformation, read trimming, alignment, variant calling, and data store migration

  • Proficiency working in Unix/Linux operating systems (BASH scripting and command line tools)

  • Proficiency in commonly used command-line NGS tools (BWA, SAMTools, Bowtie2, Picard, PINDEL, GATK, etc.)

  • Demonstrated programming and scripting skills (Perl, Python, R, C/C++, etc.)

  • Ability to understand and communicate statistical measures for interrogating the quality of data manipulation

  • Demonstrated ability to communicate efficiently and work effectively with a team of scientists

  • Demonstrated capacity for innovation

  • Experience with software development best practices: unit testing, issue tracking, software life cycle, and shared code repositories

  • Experience preparing documentation in support of CAP/CLIA certification

  • Experience with version control systems such as Git

  • Familiarity with various assays, sequencing techniques (RNA-seq, WES, WGS), and sequencing technologies from companies such as Illumina, ThermoFisher, and PacBio

  • Experience with distributed resource managers/schedulers like Univa/Sun Grid Engine (UGE/SGE) or TORQUE

  • Experience working with REST APIs

Apply Today

Join us for competitive benefits and development opportunities in a progressive and supportive environment. Help us improve our service, and the experiences of our patients and colleagues. Work with us and together we can be better.

Your Quest career. Seek it out.

All requirements are subject to possible modifications to reasonably accommodate individuals with disabilities. Quest Diagnostics is an Equal Opportunity Employer: Women / Minorities / Veterans / Disabled / Sexual Orientation / Gender Identity. *cb*