The Institute

The CNAG Consortium aims to carry out large-scale projects in DNA/RNA analysis for the improvement of quality of life in collaboration with the Spanish, European, and International Research Community. CNAG researchers participate in major International Genome Initiatives such as the Human Cell Atlas (HCA), the International Cancer Genome Consortium (ICGC), the International Human Epigenome Consortium (IHEC), the International Rare Diseases Research Consortium (IRDiRC), the European Reference Genome Atlas (ERGA), and the European Infrastructure for life-science information (ELIXIR), as well as in several EU-funded projects.

As one of the largest Genome Sequencing Centers in Europe, the Centro Nacional de Análisis Genómico (CNAG) operates Illumina NovaSeqXPlus, NS6000, MiSeqi100 sequencing systems as well as Oxford Nanopore PromethION and GridION, and Pac Bio Revio. It also regularly participates in early access programs for cutting edge sequencing technology.  Its HPC cluster features thousands of cores, Nvidia H200 GPUs and 33 Petabytes of storage, with it regularly growing to incorporate new technologies.

The Team

The Production Bioinformatics team is charged with the day to day production and processing of polished, high quality sequence data, and acts as a liaison between the sequencing laboratory, other bioinformatics teams and the CNAG collaborators. The team is managed by Matthew Ingham and is part of the CNAG Bioinformatics Analysis Unit led by Dr. Sergi Beltran.

Responsibilities include working with lab technicians, sequencer manufacturers and system administrators to maintain a stable informatics environment for the generation and processing of sequencing data by the Illumina, Pac Bio and Oxford Nanopore instruments. The team also ensures final data quality based on the review of basecalling confidence, error rates, alignment results, and coverage metadata. This is mainly done through semi-automated workflows developed and maintained by the team and running in the CNAG’s High Performance Computing (HPC) cluster. To remain on the cutting edge of next generation sequencing, the CNAG is constantly testing, upgrading and improving its instruments and protocols. Therefore, the team also conducts customised analysis and investigation, not only for specific issues and projects, but also to improve the workflows and adapt to new developments in the field. In addition, the team is responsible for developing an in-house Lab Information Management System (LIMS), which is used throughout the CNAG to track projects, samples and run information along with analysis results. The operations of the Production Bioinformatics Team are included within the CNAG ISO 9001 and ISO 27001 certifications and the ISO 17025.

These various aspects of the Production Bioinformatics team maintain the steady production of high quality data at the CNAG, and we're looking for an experienced candidate ready to contribute in this dynamic environment.

The Role

We are seeking a bioinformatician, computational biologist or software developer with knowledge of genomics to work within the Production Bioinformatics Team. The successful candidate will be responsible for the development of integrated tools and pipelines for automated processing and quality control of large amounts of Next Generation Sequencing data from a wide range of applications (Whole Genome, Exome and Panel sequencing, RNA-Seq, Methylation Sequencing, Single Cell, RNA-Seq, Genotyping-By-Sequencing, HiC, etc.), projects (inherited diseases, cancer, infectious diseases, evolution, population genomics, structural genomics, epigenetics, etc.) and organisms. The position also requires in-depth custom analysis of datasets and projects, typically for troubleshooting difficult cases or when new developments are required. Secondary tasks may include aiding the team in development of sequence alignment and variant calling pipelines, database design, and web development.

Responsabilities

• Management, processing, quality control and analysis of large amounts of Next Generation Sequencing data
• Development and/or testing of new software and solutions for the quickly changing field of DNA sequencing
• Ongoing development of the data processing and quality control pipeline on an HPC cluster
• Assure automated continuous operation and integration with the in-house developed Laboratory Information Management System (LIMS)
• Contribute to the management and development of the alignment and variant calling pipelines
• Contribute to the development of Standard Operating Procedures and the CNAG ISO certifications and accreditations (currently ISO 9001, ISO 17025 and ISO27001)
• Communication and troubleshooting with the Sequencing Unit, bioinformatics groups and CNAG collaboratos.

Requeriments

• You hold a Master’s degree in Bioinformatics or related discipline and 3+ years experience OR Bachelor’s degree with 5+ years of practical experience
• You have good knowledge of genomics
• You are very able in Unix and Windows operating systems and networks
• You have proven experience with Unix shell scripts, Python, and SQL
• You have excellent teamwork, organizational and communicative skills
• You are fluent in English

Nice to have

• You have experience in genomic data analysis
• You have experience in managing large sets of data
• You have knowledge of Perl and R, IPython and/or Matplotlib
• You have experience with batch processing on a cluster
• You have good software development practices
• You have experience in database design and web development
• You have experience with the Django database programming framework

The Offer

• Contract duration: substituion of a maternity leave with possibility to extension
• Estimated annual gross salary: Salary is commensurate with qualifications and consistent with our pay scales
• Target start date: as soon as possible

We provide a highly stimulating environment with state-of-the-art infrastructures, and unique professional career development opportunities.

We offer and promote a diverse and inclusive environment and welcomes applicants regardless of age, disability, gender, nationality, race, religion or sexual orientation.

We are committed to reconcile a work and family life for our employees and are offering the opportunity to benefit from annual leave and flexible working hours.

Aplication Procedure

All applications must be addressed to People Management - people@cnag.eu

Email subject: 2026-9 CNAG: Bioinformatician - Quality Control & Primary Analysis

Deadline: Please submit your application by 16/August/2026

All applications must include:

• A complete CV including contact details.
• Contact details of two referees.
• Cover Letter

Selection Process

The pre-selection process will be based on qualifications and expertise reflected on the candidates CVs.
Shorlisted candidates will be called for an interview.

See all our job openings in the “Jobs” section of the CNAG website: https://www.cnag.eu/jobs