Since the COVID-19 pandemic, the CNRGH has also become a key contributor to the Obépine consortium, which aims to develop wastewater-based epidemiological surveillance strategies for infectious diseases. Initially focused on SARS-CoV-2, Obépine now targets the emergence of a broad spectrum of pathogens.

In this context, we are seeking a research engineer to perform the bioinformatics analysis, interpretation of high-throughput sequencing data derived from wastewater samples and implementation of innovative approaches in viral genomics.

The candidate will:

·         Implement and optimize bioinformatics pipelines for the analysis of viral genomes from complex environmental samples, in accordance with the best practices and community guidelines.

·         Process and analyze data from multiple sequencing platforms, including Oxford Nanopore, Illumina, Element Biosciences and PacBio technologies, generated by target enrichment and/or metagenomics approach.

·         Contribute to the development of robust analytical frameworks for wastewater-based surveillance. This includes the reconstruction of viral genomes, variant analysis, haplotype assignation, and the interpretation of metagenomic data from heterogeneous and noisy samples.

·         Collaborate closely with wet lab scientists to integrate experimental design and bioinformatics analysis, to provide reporting solutions to wet lab scientists, and to support the development of innovative and reliable approaches for pathogen monitoring in wastewater.

·         Contribute to conference presentations and scientific articles, and provide a thorough reporting of bioinformatics developments.

Applicants should hold a PhD or an engineering degree in bioinformatics, computational biology, applied mathematics, or a related field, and demonstrate strong experience in one or more of the following: Python, C, C++, R, or bash. Candidates should have a proven experience with next-generation sequencing data analysis, metagenomics and/or viral genomics, and strong basis of pipeline development (such as sequence alignment, genome assembly, variant calling, and metagenomics approaches). Experience in virology, environmental genomics, statistics, or phylogenetics would be a strong advantage, as well as prior experience with high-performance computing clusters.

The position requires the ability to work effectively in a multidisciplinary environment, with strong analytical thinking, scientific rigor, autonomy, and organization skills. A strong interest in continuous scientific and technological monitoring is also expected. Good written and verbal communication skills in French and English are required.

The candidate will:

·         Implement and optimize bioinformatics pipelines for the analysis of viral genomes from complex environmental samples, in accordance with the best practices and community guidelines.

·         Process and analyze data from multiple sequencing platforms, including Oxford Nanopore, Illumina, Element Biosciences and PacBio technologies, generated by target enrichment and/or metagenomics approach.

·         Contribute to the development of robust analytical frameworks for wastewater-based surveillance. This includes the reconstruction of viral genomes, variant analysis, haplotype assignation, and the interpretation of metagenomic data from heterogeneous and noisy samples.

·         Collaborate closely with wet lab scientists to integrate experimental design and bioinformatics analysis, to provide reporting solutions to wet lab scientists, and to support the development of innovative and reliable approaches for pathogen monitoring in wastewater.

·         Contribute to conference presentations and scientific articles, and provide a thorough reporting of bioinformatics developments.

Applicants should hold a PhD or an engineering degree in bioinformatics, computational biology, applied mathematics, or a related field, and demonstrate strong experience in one or more of the following: Python, C, C++, R, or bash. Candidates should have a proven experience with next-generation sequencing data analysis, metagenomics and/or viral genomics, and strong basis of pipeline development (such as sequence alignment, genome assembly, variant calling, and metagenomics approaches). Experience in virology, environmental genomics, statistics, or phylogenetics would be a strong advantage, as well as prior experience with high-performance computing clusters.

The position requires the ability to work effectively in a multidisciplinary environment, with strong analytical thinking, scientific rigor, autonomy, and organization skills. A strong interest in continuous scientific and technological monitoring is also expected. Good written and verbal communication skills in French and English are required.

Application

This is a 19 months position, available from September 2026. Applicants are invited to send a CV, a cover letter, and contact details for two references to the following address: gerber@cnrgh.fr.