Junior Bioinformatician

Description

Job Summary: Cidacs/Fiocruz Bahia is seeking a Junior Bioinformatician to work on a national strategic project, defining architectures and implementing HPC pipelines for a national genomic data repository. Key Highlights: 1. Work on a national strategic project involving genomic data. 2. Collaborate in a technically high-complexity environment. 3. Professional development within a multidisciplinary team. Are you a **bioinformatician** early in your career, eager to learn, grow professionally, and work in a technically high-complexity environment? Do you enjoy working with genomic data, learning new tools, and contributing to solutions that will form part of a national strategic project? Then this position may be right for you. Centro de Integração de Dados e Conhecimentos para Saúde (Cidacs/Fiocruz Bahia) is recruiting a **Junior Bioinformatician** to support the Pilot of the National Genomic Data Repository under the **Genomas Brasil Program**, a priority initiative of the Ministry of Health/DECIT. You will join a multidisciplinary team responsible for building the technical, methodological, and architectural foundation for the **national repository integrating genomic, phenotypic, and clinical data** from projects funded by DECIT. Your role will be strategic: you will define architectures, implement and validate modern HPC pipelines, establish quality standards for sequences and metadata, and lead the publication of catalogs, ontologies, and versioning and reproducibility schemas — adhering to GA4GH standards and global best practices. This position is **fully remote or on-site**, at CIDACS headquarters located at Parque Tecnológico da Bahia – Edifício Tecnocentro, Rua Mundo 121, Trobogy. **Responsibilities and Duties** * **Support in designing and implementing bioinformatics pipelines**: Collaborate in developing and executing reproducible pipelines (pre\-processing, alignment, variant calling), using containers and learning international best practices (GATK Best Practices, nf\-core), always under supervision from more experienced team members. * **Support in defining QC metrics and dashboards**: Assist the team in verifying sequence (FASTQ/BAM/VCF) and clinical\-phenotypic metadata quality, helping calculate metrics, organize reports, and identify potential inconsistencies. * **Assistance in automation routines**: Contribute to creating and maintaining automated routines for data ingestion and validation, following existing models, scripts, and frameworks used by the team, focusing on standardization and efficiency. * **Support in consolidating catalogs and metadata**: Participate in organizing and updating variant and metadata catalogs, assisting with indexing, versioning, and harmonizing information according to recognized ontologies and standards. * **Collaboration in drafting Standard Operating Procedures (SOPs)**: Help prepare technical documents, guides, and templates, contributing to process standardization and reproducibility, under guidance from the technical team. * **Participation in documenting processes and pipelines**: Assist in creating and maintaining documentation for implemented solutions, ensuring clarity, organization, and team support, thereby enabling traceability and future process evolution. **Requirements and Qualifications** \- **MANDATORY QUALIFICATIONS AND REQUIREMENTS:** \- *******EDUCATION:*** * Completed undergraduate degree in Bioinformatics, Biology, Biotechnology, Computer Science, Biomedical Engineering, or related fields; OR graduate specialization/master’s degree in areas related to genomics, computational biology, or biomedical data analysis. ***EXPERIENCE:*** * Minimum one year of prior experience in bioinformatics (academic projects, scientific initiation, internships, ICs, undergraduate theses, participation in labs or research groups). * Basic experience with bioinformatics pipelines or steps (pre\-processing, alignment, variant calling). * Participation in academic or professional projects or activities involving genomic, exome, or panel data. ***TECHNICAL SKILLS:*** * Introductory knowledge of Nextflow and/or WDL/Cromwell, with willingness to deepen understanding through hands-on learning. * Familiarity with essential tools: BWA, samtools/bcftools, Picard, FastQC—even if applied only in academic contexts. * Interest and basic understanding of biomedical ontologies (HPO, SNOMED, OMOP) or clinical metadata. * Initial experience with containers (Docker or Singularity/Apptainer). * Basic knowledge of genomic data QC and curation (e.g., use of FastQC, MultiQC). * Basic knowledge of Linux environments and Shell Script. * Familiarity with Git and code versioning. * Interest in learning about HPC execution (SLURM, job queues, quotas). ***INTERPERSONAL SKILLS:*** * Strong organizational skills and commitment to continuous learning. * Analytical mindset and scientific curiosity. * Ability to collaborate effectively within multidisciplinary teams. * Clear communication and openness to receiving technical guidance. \- **DESIRED BUT NOT MANDATORY:** \- ***ADDITIONAL QUALIFICATIONS:*** * Introductory knowledge of GA4GH standards (e.g., having read or used Phenopackets, DUO, htsget). * Prior experience with tools for collecting and organizing clinical/phenotypic data (e.g., REDCap). * Basic or intermediate English proficiency for reading technical documentation. ***PREFERRED QUALIFICATIONS:*** * Academic publications, posters, or presentations at scientific conferences. * Participation in competitions, hackathons, or advanced bioinformatics courses. **Additional Information** **ABOUT THE PROJECT:** Over the next 24 months, we will transform thousands of scattered genomic sequences into a living, secure, and interoperable national repository — powered by Nextflow/WDL pipelines running on HPC, rigorous quality control, and harmonized metadata. We are building the first pilot of the National Genomic Repository, integrating genomic, phenotypic, and clinical data from projects funded by DECIT/MS, establishing the foundation for public health research, genomic surveillance, and precision medicine. We seek curious, highly technical individuals committed to open science and the ethical use of sensitive data who wish to contribute to one of the country’s most strategic initiatives in human genomics. **ABOUT CIDACS:** CIDACS is a pioneering center focused on data integration, dedicated to understanding, studying, and evaluating the health conditions of Brazil’s population using Big Data. Our work supports public managers, researchers, and the community, helping transform lives. If, like us, you are passionate about technology and innovation, join our team. Here, you will find a welcoming environment conducive to development and innovation, filled with professionals from diverse academic backgrounds united by a shared purpose. Here you will find: * A welcoming and collaborative environment; * Highly qualified and multidisciplinary professionals; * State-of-the-art infrastructure (HPC, secure data lake, TRE); * Encouragement of innovation, continuous training, and scientific autonomy. If you are passionate about bioinformatics, automation, and complex challenges, join us in this mission. Bring your talent and commitment and become part of this team! For more information about Cidacs, visit: www.cidacs.bahia.fiocruz.br Cidacs conducts studies and research based on interdisciplinary projects stemming from the linkage of large-scale datasets to expand understanding of social and environmental determinants and policies affecting population health.