Genomics Data Pipeline Analyst — HPC & Cloud

UC San Diego Health; San Diego (CA); Hybrid; USD 50,000 - 69,000; Full time

Job summary

UC San Diego Health is seeking a Research Data Analyst 2 to support sequencing analysis and genotyping across high performance computing and cloud environments. The role involves building computational pipelines, ensuring data quality, and contributing to reporting and documentation under supervision.

Under supervision, you will design workflows for sequencing analysis, organize and backup research data, and test new pipelines while selecting appropriate computational approaches.

Qualifications

• Six or more years of related experience, education, or training or a Bachelor’s degree plus two years of related experience.
• Working knowledge of research function.
• Statistical analysis, systems programming, database design, and data security measures.
• Ability to communicate complex information clearly and concisely verbally and in writing.
• Knowledge of bioinformatics software related to sequencing and genotyping.
• Experience developing multistep analysis pipelines/workflows using scripting languages including WDL.
• Experience handling big data sets and programming in R and Python.

Responsibilities

• Build computational pipelines for sequence analysis and genotyping in HPC and cloud environments.
• Run established workflows with Bash scripting and bioinformatics tools like PLINK, GATK, HipSTR, BEAGLE.
• Perform routine quality control on data inputs and analyses; assist with data organization and backup.
• Develop new pipelines under supervision and test computational approaches.
• Support data reporting tasks with moderate scope.
• Document work and annotate code; use revision control systems such as GIT.

Skills

Statistical analysis

Systems programming

Data analysis

Analysis & consultation

Communication

Bioinformatics knowledge

Linux-based workflow development

Scripting (R, Python)

Big data handling

Time management

Education

Bachelor’s degree in a related area

Tools

Bash scripting

PLINK

GATK

HipSTR

BEAGLE

WDL

R

Python

GIT

Linux

Amazon EC2

All of Us Research workbench

Bcftools

Bedtools

FastQC

Vcftools

Job description

UC San Diego Health is seeking a Research Data Analyst 2 to support sequencing analysis and genotyping across high performance computing and cloud environments. The role involves building computational pipelines, ensuring data quality, and contributing to reporting and documentation under supervision.

Under supervision, you will design workflows for sequencing analysis, organize and backup research data, and test new pipelines while selecting appropriate computational approaches.