The Hub of Bioinformatics and Biostatistics provides analytical support to research units and platforms at the Institut Pasteur. The Hub is committed to this mission through:
- Collaborating on scientific projects, submitted by research teams of our institute, to the Hub.
- Training scientific staff from the Institut Pasteur Paris or from other institutes of the international network of Instituts Pasteur.
- Developing tools and applications to be shared with the broader scientific community.
- Interacting directly with scientist upon specific inquiries.
The Hub is hiring a research engineer in bioinformatics to be detached in the BIOMICS platform to (i) manage NGS projects in all its diversity (variant calling, genome assemblies, differential analysis, etc) from the design to final reporting and (ii) develop bioinformatics analysis software within the Sequana framework (https://sequana.readthedocs.io).
The engineer will be detached for 80% of his/her time in the dry-lab group of the team headed by Marc Monot. The remaining 20% will be dedicated to technical contribution and interaction with the Hub, as well as training and teaching activities.
The Biomics technological platform (Biomics hereafter) is the C2RT structure at Institut Pasteur for Next Generation Sequencing. Our team is dedicated to Next Generation Sequencing to enable scientific discoveries within the Pasteur Institute network.
We are equipped with top-of-the-line sequencers that span short-read (Illumina, MGI) and long-read (Nanopore, PacBio) technologies, enabling us to cover a wide range of projects ( transcriptomics, genomics, genotyping, metagenomics, etc).
Our team is composed of 15 members including the dry-lab group composed of 3 bioinformaticians and a technician. This group is involved in Biomics projects throughout their life cycle from conceptualization to closure including planning (experimental design), execution (bioinformatics and biostatistics analysis), and data management. Due to an increase of activity, we are seeking a new collaborator to join our dry-lab group. As part of our team, you’ll have the opportunity to analyse lots of data and collaborate on state-of-the-art software.
Tasks and responsibilities
- Consulting during kick-off meeting to plan the bioinformatics analysis ahead. This is essential to anticipate the needs in terms of experimental design for instance.
- Perform primary and secondary analysis (from experimental designs to final reporting of the bioinformatics analysis). This includes transcriptomics, variant calling, long read assembly for example.
- Data management of the raw data
- Software development (full stack) in coordination with the team and collaborators
- Participation to national and international conferences and working groups.
Master M2, engineers and PhD in bioinformatics, computer science, computational biology are all welcome for this position, with the following skills:
- An excellent and enthusiastic Python developer. Indeed, most of our pipelines and software have been developed in Python and Snakemake framework.
- A good practice of software development is required for the position. The group will work closely together, so quick learners are welcome. Versioning using GIT is used on a daily basis.
- Excellent communication skills to interact with computer scientists, biologists, bioinformaticians, etc
Not essential but recommended for the position:
- Enjoy software development
- Enjoy the diversity of projects that will be available in this position
- Fluent in english
- Knowledge and / or experience with reproducibility framework such as Docker and Singularity will be a plus
- Knowledge of NGS secondary analysis will be a plus. Currently most of ouranalysis focuses on variant calling, assemblies, RNA-seq analysis. Implementation of other types of analyses will be encouraged.
Click on the following link and select the corresponding profile “NGS data analysis and software development” when this will be proposed:
Please, submit your updated CV and a cover letter (motivation letter). You may indicate contact information for reference letters (3 max.). They will be automatically contacted when you validate your application.
We are a team committed to foster a fair, inclusive and diverse work environment. Diversity has been scientifically established as a key factor to improve scientific objectivity. Hence, all applicants will be evaluated solely based on qualification regardless of gender, gender identity, sexual orientation, race or disability.