Assembly of heterozygous genomes

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Nom de la structure d'accueil
Adresse

Campus de Beaulieu
35000 Rennes
France

Contacts
Denis Tagu
Fabrice Legeai
Pierre Peterlongo
Email du/des contacts
denis.tagu@inra.fr
fabrice.legeai@inra.fr
pierre.peterlongo@inria.fr
Description

Context:

• INRA contract in the ITN Ignite 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.