Mots-Clés

Genome, Assembly, Annotation

Description

Bioinformatician in genome assembly

Workplace: Roscoff Biological Station, France

Contract Period: 18 months, full-time

Starting date: 1 January or February 2023

Salary: 2 200 to 2600 € gross monthly (according to experience)

Contexte

This work will be carried out in the context of the SEABIOZ ANR project with both academic partners (Roscoff Biological Station, IRISA Rennes, Natural History Museum Paris) and an industrial partner (Agro Innovation International, CMI Roullier, St. Malo). This contract is part of a multidisciplinary approach at the crossroads between massive sequence data mining, metabolomics, and system biology.

Model

Ascophyllum nodosum is a common brown alga found along the coasts of the North Atlantic Ocean. A unique feature of this alga is its mutualistic association with the fungal endophyte “Mycophycias ascophylli” and other fungi and bacteria. Very little is known so far about the importance of these symbionts for the alga, except that they are believed to protect A. nodosum from desiccation and benefit their fitness.

Fonctions

The main responsibility of the engineer will be to work on genome assembly projects of fungi and bacteria associated with the alga (A. nodosum,  whose genome assembly is already available) . The work will include genome assembly using long and short reads (mainly PacBio HiFi), but also structural and functional annotation of genomes, pipeline development. 

The engineer may be involved in comparative and/or population genomics projects. 

Responsibilities include performing analyses, communicating with partners, monitoring current developments in the field, writing reports, and potentially teaching.

Requirements

A PhD or at least three years of engineering experience, both in bioinformatics, molecular biology, computer science, or related fields considers relevant to the project position.

At least three years of experience in eukaryotic and prokaryotic genome assembly  (ideally with long-read sequencing data), as well as expertise in the use of currently used genome assemblers and assembly QC tools, including a thorough understanding of how to interpret the results. Experience with assembly curation is also required.

Ability to work effectively in a Linux command line environment.

Good communication skills, both oral and written, are required, as well as the ability to collaborate with scientists from a wide range of backgrounds.

Emphasis will be placed on personal qualities, such as the ability to lead projects and work in a collaborative environment.

A willingness to learn new methods and the ability to acquire new skills are essential for this position.

Additional Qualifications

Knowledge of genome annotation of non-model organisms and proficiency in comparative and population genomics.

Strong skills in R or scripting languages such as Python are considered.

Experience with tools used to ensure reproducibility, such as Git, containers, and workflow managers.

Applications should include a detailed CV; at least two references (persons we can contact); a one-page cover letter;

They need to be deposited at https://emploi.cnrs.fr/Offres/CDD/FR2424-BARRAF-016/Default.aspx

For further information please contact: Erwan CORRE (corre@sb-roscoff.fr)

Application deadline: date 06/12/2022