Bioinformatics Engineer - NGS Data Pipelines

Penn Medicine; Philadelphia (Philadelphia County); On-site; USD 85,000 - 120,000; Full time

Job summary

Penn Medicine in Philadelphia is seeking a Bioinformatics Specialist to maintain and execute data analysis pipelines for next-generation sequencing datasets and manage data storage on servers. The role includes developing software and custom scripts to automate data mining and manipulation.

The ideal candidate will have experience with Linux, Perl, Python, SQL, PHP, Unix shell scripting, and Excel VBA, plus familiarity with tools like BLAST for sequence data analysis.

Qualifications

• Bachelor’s degree required in Bioinformatics, Computer Science, Biology, or a related field.
• 3+ years of working knowledge of data storage and analytics related to next-generation sequencing.
• Master’s degree in Bioinformatics, Computer Science, Biology or related field preferred.

Responsibilities

• Maintains and executes clinical data analysis pipelines for all types of next-generation sequencing datasets.
• Applies knowledge and skills to perform all routine and complex data analysis for which competency has been established and authorization to perform has been granted.
• Follows all lab post-analytical procedures covering data analysis and preliminary review.
• Identifies issues/factors that adversely affect the pipeline performance and works hard to improve them.
• Takes appropriate corrective action according to established procedures, when test system performance deviates from acceptable level. Documents all corrective actions taken. Immediately notifies Supervisor or Director if unable to resolve test system problem. Ensures data is not reported until all corrective action has been taken and the pipeline is performing within specifications.
• Maintains adequate data storage levels of the servers.
• Maintains the UPS’s.
• Supports automation of pipeline and laboratory software.
• Monitors and maintains the laboratory quality control indicators to conform to all accreditation agencies.
• Assists the supervisor in specified activities that ensure laboratory compliance with all accreditation agencies.

Skills

Linux

Perl

Python

SQL

PHP

Unix shell

Excel VBA

Education

Bachelor's degree in Bioinformatics, Computer Science, Biology or related field

Master's degree in Bioinformatics, Computer Science, Biology or related field (Preferred)

Tools

BLAST

Job description

Penn Medicine in Philadelphia is seeking a Bioinformatics Specialist to maintain and execute data analysis pipelines for next-generation sequencing datasets and manage data storage on servers. The role includes developing software and custom scripts to automate data mining and manipulation.

The ideal candidate will have experience with Linux, Perl, Python, SQL, PHP, Unix shell scripting, and Excel VBA, plus familiarity with tools like BLAST for sequence data analysis.