[CPM-SPIRE-L] Engineer job offer: Assembly of heterozygous genomes

[Pierre Peterlongo]

Hi all,

Here is an engineer job offer (16 months) at Irisa, Rennes, France. We 
look forward to receiving your application!


    Context:

• INRA contract in the ITN Ignite 
<http://www.itn-ignite.eu/show/about_11570/> network. Located at Inria, 
GenScale team


    Supervision:

• Supervisor: Denis Tagu (INRA Rennes),
• Co-supervisor Fabrice Legeai (INRA Rennes) / Pierre Peterlongo (IRISA, 
Rennes)


    Context & Objectives:

Assembly of complex, very large, and highly heterozygous genomes remains 
nowadays a complex task for which no tool performs well. This is 
particularly true for insect genomes, despite countless initiatives such 
as i5K. The ITN Ignite aims among other things to propose new methods 
for assembling such non-model invertebrates.
New sequencing strategies using both short (Illumina), long reads 
(Oxford Nanopore/PacBio), linked reads (Chromium 10X), as well as 
approaches based on chromosome conformation capture (3C) are be used to 
alleviate these problems. This project will aim to develop new 
algorithms and tools for increasing the quality and the assembly of 
large and complex heterozygous genomes, while integrating data from 
diverse technologies (NGS, long reads, 3C/HiC, 10X), create new 
references structure (e.g. haplotypes in genome graphs) and further 
applications.

The applicant will be located at the INRIA/IRISA laboratory in the 
GenScale bioinformatics research team that focuses on methodological 
research at the interface between computer science and genomics. The 
main objective of this group is the design of scalable, optimized and 
parallel algorithms for processing genomic data generated by the recent 
advances of biotechnologies. This work will be based on the usage and 
development of GATB, a C++ library and software suite developed by the 
team. And, this project will benefit from the INRA IGEPP laboratory and 
their collaborators for evaluating these new strategies on various 
species with the aim to infer different traits (host recognition, 
reproduction) involved in the adaptation of target insect species to 
their environment.


    Skills

The candidate should have strong algorithmic and C++ development 
expertise. An important biological background and motivation is highly 
recommended.


    Working conditions

The recruited engineer will belong to the ETN Ignite project. Hence 
she/he will benefit from an annual workshop, from the whole ETN network 
and within planned secondments she/he will work partly abroad in the lab 
of “Jean-François Flot” (Bruxelles).


    Recruitment conditions

• The candidate should not have a PhD degree
• The candidate should be in the first four years (full-time equivalent 
research experience) of its research careers
• The candidate can be of any nationality. However, candidate’s 
residence or main activity during the 3 years prior to its recruitment 
should not be France.


    Practical aspects:

• Location: Irisa, Rennes, France.
• Start: 01/05/2019 – End: 31/07/2021


    Contacts

denis.tagu at inra.fr fabrice.legeai at inra.fr pierre.peterlongo at inria.fr




-- 
Document sans titre

*Pierre Peterlongo - INRIA* - Research Associate / Chargé de recherche
http://people.rennes.inria.fr/Pierre.Peterlongo/

Campus de Beaulieu- Rennes
35042 Rennes Cedex, France
Tel : +33 (0)2 99 84 74 59
Fax : +33 (0)2 99 84 71 71

**I do not read emails after 1pm. Call me by phone for any emergency* *

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://fenris.cs.ucr.edu/pipermail/cpm-spire-l/attachments/20190204/e286a40d/attachment.html>