PhD offer – Search engine for genomic sequencing data

в Inria
Город Rennes, France
Опубликовано 21.10.2019
Категория Биоинформатика
Тип вакансии PhD или аспирант
Адрес Campus de beaulieu


We are currently witnessing a deep knowledge revolution due to the availability of exponentially expanding DNA sequence databases. This is made possible by the continuous acceleration of DNA sequencing throughput. Sequencing data is accumulating faster than Moore’s Law, bringing fundamental new insights, conjecture, and understanding, with impacts in medicine, agronomy and ecology. Today, the Sequence Read Archive raw data archive stores more than nucleotides, in the form of short sequences ( bp) which represent fragments from generally unknown genomic location (the “reads”).

Currently there exists no way to query this treasure of information. Today, it would be unthinkable to access the Internet without powerful search engines. However, this is precisely the current situation for raw read archives, where precious data sleep undisturbed in rarely-opened drawers. In this project we propose to develop a new scaling breakthrough, allowing users to directly query sequencing data on the fly in order to tap into the largest underexploited resource in life sciences.

In the framework of the broader SeqDigger ANR project, we propose to design and propose new indexing schemes, scaling up very large DNA collection (assembled or not), and offering a way to query in real time input sequences of interest. The recruited PhD student will explore existing methods, mainly based on Bloom Filters, and will propose new algorithmic solutions.


Candidates must have strong interest and expertise in algorithmics, data structures and C++ implementation.

Knowledge in genomics and biology will be highly appreciated but is not a prerequisite.



The recruited PhD student will work in the GenScale team at Inria Rennes, France. She/he will work in close collaboration with the SeqDigger partners (Pasteur Institute Paris, CEA Genoscope, MIO) and external collaborators (EBI, Bielefeld University, …). Short stays at EBI, Cambridge, are expected.

Starting date is flexible. PhD could start as early as October 2019.

Informal enquiries are encouraged. Please contact

Applicants should send a full CV, a cover letter explaining their motivation, experience, and achievements, at least 2 references with contact information, and their date of availability.