Mots-Clés

Structural variant Copy number variation insertion deletion duplication breakends short tandem repeats filtering large variant caller

Description

Basic Function and Scope of the Position:

Illumina is the world leader in sequencing technology. While Illumina is widely used for sample kit preparation and sequencing instruments, the data workbench has taken off these last few years with the development of the DRAGEN Bio-IT platform. This platform features a wide variety of pipelines to analyze data generated by Illumina sequencers, seeking to preserve its leadership on two main advantages: superior accuracy, and extremely high speed.

DRAGEN has recently been used to re-analyze the 1000 Genome Project data from NYGC (2054 samples) on AWS generating a large amount of meaningful information.

The purpose of this internship is to focus on large variant results: Structural Variants (SV) and Copy Number Variation (CNV) and to use the information to improve precision of the DRAGEN SV and CNV callers.

The intern will translate this information into adequate additional filters and apply them to DRAGEN SV and CNV callers to decrease false positive rates. 

Offices are in Rennes with possibilities of remote/on-site work. The intern will join a growing bioinformatic team in France and work very closely with the US bioinformatic team as well. Moreover, he will be under an Illumina employee French contract with advantageous benefits.

Tasks and Responsibilities:

• Develop a good understanding of DRAGEN SV and CNV callers
• Use the output of the different DRAGEN SV and CNV callers on 1000 Genome Project data in order to build a database with event frequencies (deletions, insertions, duplications, breakends, Short Tandems Repeats, etc.)
• Identify how to classify the events in more difficult regions such as breakends
• Translate the outcome into applicable filters
• Integrate the filters into DRAGEN 
• Proceed with benchmark tests to measure impact on accuracy and performance

All listed tasks and responsibilities are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional tasks and responsibilities.

Preferred Experience/Educational Background:

• Master degree second year (MS2) in Bioinformatics or equivalent Engineering degree
• Ideally with a first degree or experience as a developer
• Very good level in English