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  • Associate Professor
  • Clinical Research Assistant
  • Full Professor
  • Graduate Student
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  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Project Manager
  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
  • Group Leader
  • Head of Facility
  • Head of Operations
  • Head of Structure
  • Honorary President of the Departement
  • Labex Coordinator
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Scientific Fields
Diseases
Organisms
Applications
Technique
Starting Date
01
Mar 2019
Ending Date
08
Sep 2020
Status
Completed
Members
2
Structures
3
Publications
1

About

Linked-reads are a valuable technologies laying in between short reads and long reads. LR technologies allow the simulation of long reads using barcoded short reads.

But the chemistry of such technologies have a limitation due to the limited amount of barcodes.
Multiple molecules can share the same tag. So resulting short reads can’t be assigned to a precise molecule.

In this project we analyze underlying graph properties of the barcodes and molecules.
We proposed a totally new approach based on a new object called Local Clique Pair (LCP) to analyse the molecules from linked reads sequencing.

In a paper accepted to WABI 2020, we describe an algorithm to create the LCPs from sequencing data and a heuristic to order them reflecting the order of the molecules along simulated genomes.

These datastructures and algorithms answer 2 linked reads question:

  • How many molecules are present in each barcode ?
  • Can we construct a partial order of the molecules along pieces of the genome ?