Bioinformatics pipeline developer
Pubblicato: 10.04.2025
Chiusura: 31.05.2025
Bioinformatics pipeline developer in the Candiolo Genomics Centre (CGC) jointly developed by the Candiolo Cancer Institute FPO – IRCCS and the Italian Institute of Genomic Medicine (IIGM).
Background
The Candiolo Cancer Institute FPO – IRCCS is a private non-profit institution founded and supported by the Fondazione Piemontese per la Ricerca sul Cancro-Onlus (FPRC) and operated by the Fondazione del Piemonte per l’Oncologia (FPO) with the mission of contributing to fight cancer by conducting state-of-the-art research, diagnostic, and therapeutic activities.
The Italian Institute of Genomic Medicine (IIGM) is a private non-profit research foundation established by ‘Fondazione Compagnia di San Paolo’ in Turin, whose core mission is conducting excellent research and training in the fields of human genomics and epigenomics, systems biology, immunology, and bioinformatics.
FPO and IIGM are currently integrating their next-generation sequencing (NGS) facilities and establishing a shared high-performance computing (HPC) cluster, with the goal of developing a Candiolo Genomics Centre whose mission will be hosting and maintaining state-of-the-art NGS platforms, offering cutting-edge services to local and external research groups, as well as conducting genomic data-driven research programs targeting unmet clinical needs.
Position Summary
FPO and IIGM are looking for a Bioinformatics pipeline Developer to design, implement, and maintain bioinformatics workflows for NGS data analysis. The successful candidate will be embedded in the Bioinformatics Unit that we plan to establish within the Candiolo Genomics Centre and report to the Head of the Bioinformatics Unit. The position will serve as a critical bridge between the sequencing facility and research teams, ensuring efficient, high-quality data processing and analysis.
The successful candidate will work closely with sequencing specialists, bioinformaticians, and research groups to develop scalable, reproducible, and automated pipelines for analysing diverse NGS datasets, including data generated by short- and long-read whole-genome sequencing (WGS), whole-exome sequencing (WES), short- and long-read RNA-seq, single-cell DNA/RNA sequencing, epigenomic assays ((sc)ATAC-seq, CUT&Run, Hi-C, …), and spatial transcriptomics.
Key Responsibilities
- Develop and maintain automated bioinformatics pipelines for processing sequencing data generated by the Sequencing Core Facility.
- Collaborate with the staff of the Sequencing Core Facility to ensure high-throughput, high-quality data processing and troubleshoot issues in real time.
- Implement workflows using Nextflow to ensure scalability and reproducibility.
- Optimize pipelines for the HPC.
- Ensure rigorous quality control checks and data integrity before delivery to research teams.
- Maintain detailed documentation and provide training/support for researchers using sequencing data.
- Stay updated on advancements in NGS technologies and collaborate on method development with the sequencing facility.
- Assist in developing best practices for data management, reproducibility, and regulatory compliance.
- Manage genomic data deposition to public archives such as GEO, SRA, ENA, etc. for publications originating from intramurally funded projects.
Required Qualifications
- MSc or PhD in Bioinformatics, Computational Biology, Computer Science, or a related field.
- Strong programming skills in Bash, Python and/or R.
- Experience with workflow management tools (e.g., Nextflow, Snakemake, WDL/Cromwell).
- Familiarity with HPC environments and containerization (Docker, Singularity).
- Strong understanding of commonly used NGS technology platforms and NGS assays.
- Experience with version control systems (GitHub/GitLab) and CI/CD workflows.
- Ability to communicate effectively and work collaboratively with wet lab scientists, sequencing facility staff, and research teams.
Preferred Qualifications
- Prior experience working directly with a sequencing core facility or large-scale sequencing projects.
- Prior experience developing custom pipelines, e.g., for single-cell, long-read or spatial omic assays.
- Experience providing bioinformatics training and support to researchers.
- Familiarity with LIMS (Laboratory Information Management Systems) for tracking sequencing runs and metadata.
Application process
To apply for this position, please send an e-mail to nicola.crosetto@ircc.it with the subject ‘FPO-IIGM Pipeline developer 2025’ and the following documents attached:
- A 1-page motivation letter (in English, pdf format) in pdf format describing past and present work experiences and key motivations for applying to this position.
- An up-to-date Curriculum Vitae (in English, max 2 pages, pdf format)
- A list of publications (if available) in reverse chronological order, marking those most relevant for this application (max 5 pages, pdf format)
Offered positions: no. 01 – available immediately.
Offered contract: 1 yr. co.co.co. (retribution level depending on entry-level experience) with possibility of further extension(s).
For questions regarding the position and application process, please contact nicola.crosetto@ircc.it.
Please send your application no later than May 15, 2025.
