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  • center
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  • nrc
  • whocc
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  • tool
  • patent
  • Administrative Staff
  • Assistant Professor
  • Associate Professor
  • Clinical Research Assistant
  • Clinical Research Nurse
  • Clinician Researcher
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  • Lab assistant
  • Master Student
  • Non-permanent Researcher
  • Nursing Staff
  • Permanent Researcher
  • Pharmacist
  • PhD Student
  • Physician
  • Post-doc
  • Prize
  • 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
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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 ?